Dissertations / Theses on the topic 'Computational Reaction Kinetics'

A deep understanding of molecular reactions is a challenging task since the range of time and energy covered implies a wide and dense grid for the numerical representation of the reactive Hamiltonian. For a computational chemist, the accurate prediction of its value starting from the definition of reactants and products is fascinating and demanding, but can be extremely useful for further investigation and optimization problems. Several methods, all derived by the Transition State Theory, have been developed to avoid the computational cost of the Hamiltonian representation on a large, multidimensional grid; we investigate these strategies both in the time and energy domain to explore the advan- tages and drawbacks of these reciprocal spaces. Since we want to increase the range of applicability of the calcula- tion of thermal rate constants to medium size molecules, which can have floppy geometries with low frequency modes, we introduce a dedicated treatment of such modes based on the Intrinsic Reaction Path of Fukui. In Part i, we introduce the theoretical instrument used to perform our calculation, both in energy and time domain; Part ii is devoted to the presentation of the applications, mainly focused on current issues in astrochemical studies. Appendices treat specific topics, like Möller operators, essential for the comprehension of the theory but too long to be inserted in Part i.

In the last two decades, Computational Fluid Dynamics (CFD) has shown great potential as a powerful and cost-efficient tool to troubleshoot existing disinfection contactors and improve future designs for the water and wastewater treatment utilities. In the first part of this dissertation two CFD simulation methodologies or strategies for computing turbulent flow are evaluated in terms of the predicted hydraulic performance of contactors. In the LES (large eddy simulation) methodology, the more energetic, larger scales of the turbulence are explicitly computed or resolved by the grid. In the less computationally intensive RANS (Reynolds-averaged Navier-Stokes) methodology, only the mean component of the flow is resolved and the effect of the unresolved turbulent scales is accounted for through a turbulence model. For baffled contactors, RANS performs on par with the LES in predicting hydraulic performance indices. In this type of contactors, hydraulic performance is primarily determined by quasi-steady recirculating (dead) zones within the contactor chambers which are well-resolved in both RANS and LES. Testing of the RANS methodology is also performed for a wastewater stabilization pond leading to prediction of hydraulic performance indices in good agreement with field measurements. However, for column contactors, LES performs better than RANS due to the ability of the LES to resolve unsteady or unstable flow structure associated with spatial transition to turbulence which is important in the determination of the hydraulic performance of the contactor. In the second part of this dissertation the RANS methodology is adapted in order to develop a novel modeling framework for ozone disinfection of drinking water. This framework is unique as it combines CFD with kinetics-based reaction modeling to predict disinfection performance and bromate formation for the first time. Bromate, a human health hazard, is an undesired by-product of the disinfection of drinking water via ozonation. The modeling framework is validated via application to a full-scale ozone contactor. Predictions of ozone and bromate concentrations are consistent with data from physical experiments.

In order to better understand the kinetics of gas phase bimolecular exchange reactions a computer program has been written which allows easy exploration of the time dependent and vibrational level dependent details of this class of reactions. BIMSIM (for BIMolecular exchange reaction SIMulation) is intended as a very flexible "virtual laboratory" which can easily be configured and reconfigured for a wide range of different experiments (e.g., laser pulse or shock tube), different initial conditions (e.g., of temperature, reactant concentration, and molecular environment), for different reactions in this class, and for different levels of approximation. In order to test the validity and demonstrate the use of the program a reaction system was found for which appropriate input data is available and for which suitably detailed analytical calculations have been done. Agreement was found to be excellent. Using BIMSIM, results of chemical interest were obtained for the reaction Br + HCl $\to$ HBr + Cl. It was found that non-equilibrium depletion of the vibrational levels of HCl are as much as a factor of 10 and that they depend on the relative amounts of Br, HCl and inert diluent He, as well as on the temperature, becoming more pronounced around 500 K. Interesting details of the time dependence of the fractional level populations are discussed.

Biosensors are analytical devices made up of a combination of a biological entity, usually an enzyme, that recognizes a specific analyte (substrate) and the transducer that translates the biorecognition event into a signal. In order to create new types of biosensors the corresponding experimental studies are necessary. Computational experiments could very well replace very expensive physical ones. However, the multi-step character of a chemical reaction scheme must be considered and modeled accordingly. In this thesis such reaction schemes were studied in great details. Original mathematical models were developed for optical peroxidase-based and amperometric laccase-based biosensors. The deterministic nature of model construction allows the automated models to be built. Based on this assumption flexible model for computational modeling of different practical multistep biosensors was developed. In order to optimize the numerical solution of the reaction-diffusion type equations common finite difference schemes were compared. The comparison shows that the fastest schemes to achieve the required relative error are implicit and Hopscotch schemes. For the problems where accuracy is not a significant factor but the speed is, the simplest explicit scheme should be used. Applying the new flexible model a computational modeling of the multi-step biosensors were produced. The modeling of laccase biosensor explained and confirmed the synergistic effect. The computational modeling of the... [to full text]
Biojutikliai yra analitiniai įtaisai sudaryti iš biologiškai aktyvios bei selektyviai atpažįstančios substratą medžiagos, dažniausiai fermento, ir keitiklio formuojančio makroskopinį fizinį signalą. Naujų įtaisų kūrimui būtini lygiagretūs eksperimentiniai tyrimai. Skaitiniai eksperimentai gali patikimai pakeisti fizinius. Modeliuojant tokius biojutiklius, būtina atsižvelgti į juose vykstančių procesų daugiapakopį pobūdį. Šiame darbe nuodugniai ištirtos tokių reakcijų schemų savybės. Sudaryti originalūs matematiniai modeliai optiniam peroksidaziniam bei amperometriniam lakaziniam daugiapakopiams biojutikliams. Deterministinė modelių sudarymo proceso prigimtis leidžia jį automatizuoti. Remiantis šiuo principu sukurtas bendras įrankis kompiuteriniam daugiapakopių biojutiklių modeliavimui. Siekiant optimizuoti skaitinį sprendimą palygintos dažniausiai naudojamos baigtinių skirtumų skaitinio sprendimo schemos sprendžiant reakcijos - difuzijos lygtis. Pastarasis palyginimas parodė, kad greičiausiai reikiamas sprendinio tikslumas pasiekiamas taikant neišreikštinę bei Hopscotch schemas. Uždaviniams, kuriems sparta svarbesnė už tikslumą, turėtų būti taikoma išreikštinė schema. Taikant naują įrankį atliktas kompiuterinis daugiapakopių biojutiklių modeliavimas. Kompiuterinis lakazinio biojutiklio modeliavimas teoriškai paaiškino eksperimentiškai stebėtą sinergetinę mediatoriaus įtaką biojutiklio atsakui. Peroksidazinio biojutiklio kompiuterinio modeliavimo rezultatai parodė, kad plataus... [toliau žr. visą tekstą]

In this thesis a reduced dimensionality quantum scattering model is applied to the study of polyatomic reactions of type X + CH4 <--> XH + CH3. Two dimensional quantum scattering of the symmetric hydrogen exchange reaction CH3+CH4 <--> CH4+CH3 is performed on an 18-parameter double-Morse analytical function derived from ab initio calculations at the CCSD(T)/cc-pVTZ//MP2/cc-pVTZ level of theory. Spectator mode motion is approximately treated via inclusion of curvilinear or rectilinear projected zero-point energies in the potential surface. The close-coupled equations are solved using R-matrix propagation. The state-to-state probabilities and integral and differential cross sections show the reaction to be primarily vibrationally adiabatic and backwards scattered. Quantum properties such as heavy-light-heavy oscillating reactivity and resonance features significantly influence the reaction dynamics. Deuterium substitution at the primary site is the dominant kinetic isotope effect. Thermal rate constants are in excellent agreement with experiment. The method is also applied to the study of electronically nonadiabatic transitions in the CH3 + HCl <--> CH4 + Cl(2PJ) reaction. Electrovibrational basis sets are used to construct the close-coupled equations, which are solved via Rmatrix propagation using a system of three potential energy surfaces coupled by spin-orbit interaction. Ground and excited electronic surfaces are developed using a 29-parameter double-Morse function with ab initio data at the CCSD(T)/ccpV( Q+d)Z-dk//MP2/cc-pV(T+d)Z-dk level of theory, and with basis set extrapolated data, both corrected via curvilinear projected spectator zero-point energies. Coupling surfaces are developed by fitting MCSCF/cc-pV(T+d)Z-dk ab initio spin orbit constants to 8-parameter functions. Scattering calculations are performed for the ground adiabatic and coupled surface models, and reaction probabilities, thermal rate constants and integral and differential cross sections are presented. Thermal rate constants on the basis set extrapolated surface are in excellent agreement with experiment. Characterisation of electronically nonadiabatic nonreactive and reactive transitions indicate the close correlation between vibrational excitation and nonadiabatic transition. A model for comparing the nonadiabatic cross section branching ratio to experiment is discussed.

The gas phase reactions of atomic chlorine with hydrogen sulfide, ammonia, benzene, and ethylene are investigated using the laser flash photolysis / resonance fluorescence experimental technique. In addition, the kinetics of the reverse processes for the latter two elementary reactions are also studied experimentally. The absolute rate constants for these processes are measured over a wide range of conditions, and the results offer new accurate information about the reactivity and thermochemistry of these systems. The temperature dependences of these reactions are interpreted via the Arrhenius equation, which yields significantly negative activation energies for the reaction of the chlorine atom and hydrogen sulfide as well as for that between the phenyl radical and hydrogen chloride. Positive activation energies which are smaller than the overall endothermicity are measured for the reactions between atomic chlorine with ammonia and ethylene, which suggests that the reverse processes for these reactions also possess negative activation energies. The enthalpies of formation of the phenyl and β-chlorovinyl are assessed via the third-law method. The stability and reactivity of each reaction system is further rationalized based on potential energy surfaces, computed with high-level ab initio quantum mechanical methods and refined through the inclusion of effects which arise from the special theory of relativity. Large amounts of spin-contamination are found to result in inaccurate computed thermochemistry for the phenyl and ethyl radicals. A reformulation of the computational approach to incorporate spin-restricted reference wavefunctions yields computed thermochemistry in good accord with experiment. The computed potential energy surfaces rationalize the observed negative temperature dependences in terms of a chemical activation mechanism, and the possibility that an energized adduct may contribute to product formation is investigated via RRKM theory.

This PhD thesis focuses on the theoretical and computational modeling of gas phase chemical reactions, with a particular emphasis on astrophysical and atmospherical ones. The ability to accurately determine the rate coefficients of key elementary reactions is deeply connected to the accurate determination of geometrical parameters, vibrational frequencies and, even more importantly, electronic energies and zeropoint energy corrections of reactants, transition states, intermediates and products involved in the chemical reaction, together with a suitable choice of the statistical approach for the rate computation (i.e. the proper transition state theory model). The main factor limiting the accuracy of this process is the computational time requested to reach meaningful results (i.e. reaching subchemical accuracy below 1 kJ mol−1), which increases dramatically with the the size of the system under investigation. For small-sized systems, several nonempirical procedures have been developed and presented in the literature. However, for larger systems the well-known model chemistries are far from being parameter-free since they include some empirical parameters and employ geometries which are not fully reliable for transition states and noncovalent complexes possibly ruling the entrance channels. Based on these premises, this dissertation has been focused on the development of new “cheap” composite schemes, entirely based on the frozen core coupled cluster ansatz including single, double, and (perturbative) triple excitation calculations in conjunction with a triple-zeta quality basis set, including the contributions due to the extrapolation to the complete basis set limit and core-valence effects using second-order Møller- Plesset perturbation theory. For the first time the “cheap” scheme has been extended to explicitly-correlated methods, which have an improved performance with respect to their conventional counterparts. Benchmarks with different sets of state of the art energy barriers, interaction energies and geometrical parameters spanning a wide range of values show that, in the absence of strong multireference contributions, the proposed models outperforms the most well-known model chemistries, reaching a subchemical accuracy without any empirical parameter and with affordable computer times. Besides the composite schemes development efforts, a robust protocol for disclosing the thermochemistry and kinetics of reactions of atmospheric and astrophysical interest, rooted in the so-called ab initio-transition-state-theory-based master equation approach have been thoroughly investigated and validated.

This thesis presents an experimental and theoretical study of the collision dynamics of OH(A²Σ⁺) with Kr and Xe. These two systems both exhibit a significant degree of electronically non-adiabatic behaviour, and a particular emphasis of the work presented here is to characterise the competition and interplay between electronic quenching on the one hand, and electronically adiabatic collisional processes on the other. Quenching takes place close to the bottom of the deepest potential well for both systems. In collisions that remain in the excited electronic state, this same region of the potential is also largely responsible for rotational energy transfer (RET) and the collisional depolarisation of angular momentum. Therefore, the direct competition between these processes suppresses the cross-sections for RET and collisional depolarisation from their expected value in the absence of quenching. To investigate this, experiments were carried out to measure cross-sections for the collisional transfer of electronic, vibrational and rotational energy in OH(A, v=0,1) + Kr and OH(A, v=0) + Xe. In addition, measurements were made of the j-j' correlation -- that is, the relationship between the angular momentum of the OH radical before and after a collision -- in collisions with Kr and Xe, using the experimental technique of Zeeman quantum beat spectroscopy. Collisions with both Kr and Xe tend to effectively depolarise the angular momentum of the OH radical, due to the very anisotropic character of the potential on which the process occurs. Electronic quenching, which plays an essential role in both systems, is more prevalent with xenon as the crossing to the ground state potential is located in a more accessible location. These experimental results were compared with single surface quasi-classical trajectory (QCT) calculations, where the overestimate of rotational energy transfer or collisional depolarisation helps to elucidate the degree to which the presence of quenching suppresses these processes. Surface hopping QCT was then used to account for non-adiabatic transitions in the theory, which led to an improvement in agreement with experiment. However, standard surface hopping QCT theory failed to account for the full extent of quenching in these two systems. A major focus of this work is therefore on the development of an extension to standard surface hopping QCT theory to incorporate rovibronic couplings. In non-linear configurations, the excited state of the OH + Kr, Xe systems has A' symmetry, while the ground state is split into symmetric (A') and antisymmetric (A'') components. For these symmetry reasons, coupling is restricted to the two states of the same symmetry, however a rotation of the correct (A'') symmetry can induce transitions to the A'' state too. Inclusion of all three electronic states, and the relevant couplings between them, is found to be crucial for a proper description of experimental reality.

Doctor of Philosophy
Department of Chemical Engineering
Bin Liu
Efficient and selective catalysis lies at the heart of many chemical reactions, enabling the synthesis of chemicals and fuels with enormous societal and technological impact. A fundamental understanding of intrinsic catalyst properties for effective manipulation of the reactivity and selectivity of industrial catalysts is essential to select proper catalysts to catalyze the reactions we want and hinder the reactions we do not want. The progress in density functional theory (DFT) makes it possible to describe interfacial catalytic reactions and predict catalytic activities from one catalyst to another. In this study, water-gas shift reaction (WGSR) was used as a model reaction. First-principles based micro-kinetic modeling has been performed to deeply understand interactions between competing reaction mechanisms, and the relationship with various factors such as catalyst materials, structures, promoters, and interactions between intermediates (e.g., CO self-interaction) that govern the observed catalytic behaviors. Overall, in this thesis, all relevant reaction mechanisms in the model reaction on well-defined active sites were developed with first-principles calculations. With the established mechanism, the promotional effect of K adatom on Ni(111) on WGSR compared to the competing methanation was understood. Moreover, the WGSR kinetic trend, with the hydrogen production rate decreasing with increasing Ni particle diameters (due to the decreasing fractions of low-coordinated surface Ni site), was reproduced conveniently from micro-kinetic modeling techniques. Empirical correlations such as Brønsted-Evans-Polanyi (BEP) relationship for O-H, and C-O bond formation or cleavage on Ni(111), Ni(100), and Ni(211) were incorporated to accelerate computational analysis and generate trends on other transition metals (e.g., Cu, Au, Pt). To improve the numerical quality of micro-kinetic modeling, later interactions of main surface reaction intermediates were proven to be critical and incorporated successfully into the kinetic models. Finally, evidence of support playing a role in the enhancement of catalyst activity and the impact on future modeling will be discussed. DFT will be a powerful tool for understanding and even predicting catalyst performance and is shaping our approach to catalysis research. Such molecular-level information obtained from computational methods will undoubtedly guide the design of new catalyst materials with high precision.

Biojutikliai yra analitiniai įtaisai sudaryti iš biologiškai aktyvios bei selektyviai atpažįstančios substratą medžiagos, dažniausiai fermento, ir keitiklio formuojančio makroskopinį fizinį signalą. Naujų įtaisų kūrimui būtini lygiagretūs eksperimentiniai tyrimai. Skaitiniai eksperimentai gali patikimai pakeisti fizinius. Modeliuojant tokius biojutiklius, būtina atsižvelgti į juose vykstančių procesų daugiapakopį pobūdį. Šiame darbe nuodugniai ištirtos tokių reakcijų schemų savybės. Sudaryti originalūs matematiniai modeliai optiniam peroksidaziniam bei amperometriniam lakaziniam daugiapakopiams biojutikliams. Deterministinė modelių sudarymo proceso prigimtis leidžia jį automatizuoti. Remiantis šiuo principu sukurtas bendras įrankis kompiuteriniam daugiapakopių biojutiklių modeliavimui. Siekiant optimizuoti skaitinį sprendimą palygintos dažniausiai naudojamos baigtinių skirtumų skaitinio sprendimo schemos sprendžiant reakcijos - difuzijos lygtis. Pastarasis palyginimas parodė, kad greičiausiai reikiamas sprendinio tikslumas pasiekiamas taikant neišreikštinę bei Hopscotch schemas. Uždaviniams, kuriems sparta svarbesnė už tikslumą, turėtų būti taikoma išreikštinė schema. Taikant naują įrankį atliktas kompiuterinis daugiapakopių biojutiklių modeliavimas. Kompiuterinis lakazinio biojutiklio modeliavimas teoriškai paaiškino eksperimentiškai stebėtą sinergetinę mediatoriaus įtaką biojutiklio atsakui. Peroksidazinio biojutiklio kompiuterinio modeliavimo rezultatai parodė, kad plataus... [toliau žr. visą tekstą]
Biosensors are analytical devices made up of a combination of a biological entity, usually an enzyme, that recognizes a specific analyte (substrate) and the transducer that translates the biorecognition event into a signal. In order to create new types of biosensors the corresponding experimental studies are necessary. Computational experiments could very well replace very expensive physical ones. However, the multi-step character of a chemical reaction scheme must be considered and modeled accordingly. In this thesis such reaction schemes were studied in great details. Original mathematical models were developed for optical peroxidase-based and amperometric laccase-based biosensors. The deterministic nature of model construction allows the automated models to be built. Based on this assumption flexible model for computational modeling of different practical multistep biosensors was developed. In order to optimize the numerical solution of the reaction-diffusion type equations common finite difference schemes were compared. The comparison shows that the fastest schemes to achieve the required relative error are implicit and Hopscotch schemes. For the problems where accuracy is not a significant factor but the speed is, the simplest explicit scheme should be used. Applying the new flexible model a computational modeling of the multi-step biosensors were produced. The modeling of laccase biosensor explained and confirmed the synergistic effect. The computational modeling of the... [to full text]

This work investigates the computer modelling of the photochemical formation of smog products such as ozone and aerosol, in a system containing toluene, NOx and water vapour. In particular, the problem of modelling this process in the Commonwealth Scientific and Industrial Research Organization (CSIRO) smog chambers, which utilize outdoor exposure, is addressed. The primary requirement for such modelling is a knowledge of the photolytic rate coefficients. Photolytic rate coefficients of species other than N02 are often related to JNo2 (rate coefficient for the photolysis ofN02) by a simple factor, but for outdoor chambers, this method is prone to error as the diurnal profiles may not be similar in shape. Three methods for the calculation of diurnal JNo2 are investigated. The most suitable method for incorporation into a general model, is found to be one which determines the photolytic rate coefficients for N02, as well as several other species, from actinic flux, absorption cross section and quantum yields. A computer model was developed, based on this method, to calculate in-chamber photolysis rate coefficients for the CSIRO smog chambers, in which ex-chamber rate coefficients are adjusted by accounting for variation in light intensity by transmittance through the Teflon walls, albedo from the chamber floor and radiation attenuation due to clouds. The photochemical formation of secondary aerosol is investigated in a series of toluene-NOx experiments, which were performed in the CSIRO smog chambers. Three stages of aerosol formation, in plots of total particulate volume versus time, are identified: a delay period in which no significant mass of aerosol is formed, a regime of rapid aerosol formation (regime 1) and a second regime of slowed aerosol formation (regime 2). Two models are presented which were developed from the experimental data. One model is empirically based on observations of discrete stages of aerosol formation and readily allows aerosol growth profiles to be calculated. The second model is based on an adaptation of published toluene photooxidation mechanisms and provides some chemical information about the oxidation products. Both models compare favorably against the experimental data. The gross effects of precursor concentrations (toluene, NOx and H20) and ambient conditions (temperature, photolysis rate) on the formation of secondary aerosol are also investigated, primarily using the mechanism model. An increase in [NOx]o results in increased delay time, rate of aerosol formation in regime 1 and volume of aerosol formed in regime 1. This is due to increased formation of dinitrocresol and furanone products. An increase in toluene results in a decrease in the delay time and an increase in the rate of aerosol formation in regime 1, due to enhanced reactivity from the toluene products, such as the radicals from the photolysis of benzaldehyde. Water vapor has very little effect on the formation of aerosol volume, except that rates are slightly increased due to more OH radicals from reaction with 0(1D) from ozone photolysis. Increased temperature results in increased volume of aerosol formed in regime 1 (increased dinitrocresol formation), while increased photolysis rate results in increased rate of aerosol formation in regime 1. Both the rate and volume of aerosol formed in regime 2 are increased by increased temperature or photolysis rate. Both models indicate that the yield of secondary particulates from hydrocarbons (mass concentration aerosol formed/mass concentration hydrocarbon precursor) is proportional to the ratio [NOx]0/[hydrocarbon]0

Animal cells are often cultured in stirred tank reactors. Having no cell wall, these animal cells are very sensitive to the fluid mechanical stresses that result from agitation by the impeller and from the rising and bursting of bubbles, which are generated within the culture medium in the stirred tank to supply oxygen by mass transfer to the cells. If excessive, these fluid mechanical stresses can result in damage/death of animal cells. Stress due to the rising and bursting of bubbles can be avoided by using a gas-permeable membrane, in the form of a long coiled tube (with air passing through it) within the stirred tank, instead of air-bubbles to oxygenate the culture medium. Fluid mechanical stress due to impeller agitation can be controlled using appropriate impeller rotational speeds. The aim of this study was to lay the foundations for future work in which a correlation would be developed between cell damage/death and the fluid mechanical stresses that result from impeller agitation and bubbling. Such a correlation could be used to design stirred-tank reactors at any scale and to determine appropriate operating conditions that minimise cell damage/death due to fluid mechanical stresses. Firstly, a validated CFD model of a baffled tank stirred with a Rushton turbine was developed to allow fluid mechanical stresses due to impeller agitation to be estimated. In these simulations, special attention was paid to the turbulence energy dissipation rate, which has been closely linked to cell damage/death in the literature. Different turbulence models, including the k-ε, SST, SSG-RSM and the SAS-SST models, were investigated. All the turbulence models tested predicted the mean axial and tangential velocities reasonably well, but under-predicted the decay of mean radial velocity away from the impeller. The k-ε model predicted poorly the generation and dissipation of turbulence in the vicinity of the impeller. This contrasts with the SST model, which properly predicted the appearance of maxima in the turbulence kinetic energy and turbulence energy dissipation rate just off the impeller blades. Curvature correction improved the SST model by allowing a more accurate prediction of the magnitude and location of these maxima. However, neither the k-ε nor the SST models were able to properly capture the chaotic and three-dimensional nature of the trailing vortices that form downstream of the blades of the impeller. In this sense, the SAS-SST model produced more physical predictions. However,this model has some drawbacks for modelling stirred tanks, such as the large number of modelled revolutions required to obtain good statistical averaging for calculating turbulence quantities. Taking into consideration both accuracy and solution time, the SSG-RSM model was the least satisfactory model tested for predicting turbulent flow in a baffled stirred tank with a Rushton turbine. In the second part of the work, experiments to determine suitable oxygen transfer rates for culturing cells were carried out in a stirred tank oxygenated using either a sparger to bubble air through the culture medium or a gas-permeable membrane. Results showed that the oxygen transfer rates for both methods of oxygenation were always above the minimum oxygen requirements for culturing animal cells commonly produced in industry, although the oxygen transfer rate for air-bubbling was at-least 10 times higher compared with using a gas-permeable membrane. These results pave the way for future experiments, in which animal cells would be cultured in the stirred tank using bubbling and (separately) a gas-permeable membrane for oxygenation so that the effect of rising and bursting bubbles on cell damage/death rates can be quantified. The effect of impeller agitation on cell damage/death would be quantified by using the gas permeable membrane for oxygenation (to remove the detrimental effects of bubbling), and changing the impeller speed to observe the effect of agitation intensity. In the third and final part of this work, the turbulent flow in the stirred tank used in the oxygenation experiments was simulated using CFD. The SST turbulence model with curvature correction was used in these simulations, since it was found to be the most accurate model for predicting turbulence energy dissipation rate in a stirred tank. The predicted local maximum turbulence energy dissipation rate of 8.9x10¹ m2/s3 at a rotational speed of 900 rpm was found to be substantially less than the value of 1.98x10⁵ m2/s3 quoted in the literature as a critical value above which cell damage/death becomes significant. However, the critical value for the turbulence energy dissipation rate quoted in the literature was determined in a single-pass flow device, whereas animal cells in a stirred tank experience frequent exposure to high turbulence energy dissipation rates (in the vicinity of the impeller) due to circulation within the stirred tank and long culture times. Future cell-culturing experiments carried out in the stirred tank of this work would aim to determine a more appropriate critical value for the turbulence energy dissipation rate in a stirred tank, above which cell damage/death becomes a problem.

This thesis primarily focuses on the electrochemical properties of the H₂/H⁺ redox couple, at various metallic electrodes in room temperature ionic liquids. Initially, a comprehensive overview of room temperature ionic liquids, RTILs, compared to conventional organic solvents is presented which identifies their favourable properties and applications, followed by a second chapter describing the basic theory of electrochemistry. A third chapter presents the general experimental reagents, instruments and measurements used in this thesis. The results presented in this thesis are summarized in six further chapters and shown as follows. (1) Hydrogenolysis, hydrogen loaded palladium electrodes by electrolysis of H[NTf₂] in a RTIL [C₂mim][NTf₂]. (2) Palladium nanoparticle-modified carbon nanotubes for electrochemical hydrogenolysis in RTILs. (3) Electrochemistry of hydrogen in the RTIL [C₂mim][NTf₂]: dissolved hydrogen lubricates diffusional transport. (4) The hydrogen evolution reaction in a room temperature ionic liquid: mechanism and electrocatalyst trends. (5) The formal potentials and electrode kinetics of the proton_hydrogen couple in various room temperature ionic liquids. (6) The electroreduction of benzoic acid: voltammetric observation of adsorbed hydrogen at a Platinum microelectrode in room temperature ionic liquids. The first two studies show electrochemically formed adsorbed H atoms at a metallic Pt or Pd surface can be used for clean, efficient, safe electrochemical hydrogenolysis of organic compounds in RTIL media. The next study shows the physicochemical changes of RTIL properties, arising from dissolved hydrogen gas. The last three studies looked at the electrochemical properties of H₂/H⁺ redox couple at various metallic electrodes over a range of RTILs vs a stable Ag/Ag⁺ reference couple, using H[NTf₂] and benzoic acid as proton sources. The kinetic and thermodynamic mechanisms of some reactions or processes are the same in RTILs as in conventional organic or aqueous solvents, but other remarkably different behaviours are presented. Most importantly significant constants are seen for platinum, gold and molybdenum electrodes in term of the mechanism of proton reduction to form hydrogen.

Thesis (Ph.D.)--Case Western Reserve University, 2009
Abstract Department of Mechanical and Aerospace Engineering Title from PDF (viewed on 14 April 2009) Available online via the OhioLINK ETD Center

Detailed chemical kinetic models are important to the understanding and prediction of combustion properties. Better estimations require an accurate description of thermochemistry and kinetic rate parameters. This study identifies important reaction pathways at the low temperature chemistry of branched conventional and alternative fuels. Rate constants and branching ratios for important reactions are provided and important phenomena are investigated. The thermochemistry and kinetics of the 2-methylhexane model, an important component in gasoline surrogate, is updated using recent group values and rate rules from the literature. New reactions, such as hydroperoxyalkylperoxy (OOQOOH) alternative isomerization, are also added to the model. The results show that both conventional and alternative isomerization of OOQOOH radicals significantly affect the model reactivity. The kinetics of a biofuel; iso-butanol, is also investigated in this study to understand alcohol combustion chemistry and identify sensitive reactions that require more attention. The results indicate that iso-butanol is sensitive to the chain propagation reaction of α-RO2 radical and the water elimination of γ-QOOH. Because both reactions decrease model reactivity, accurate rate constants are needed to correctly determine fuel reactivity. In light of the above mentioned kinetic modeling studies, high levels computational chemistry calculations were performed to provide site-specific rates rules for OOQOOH conventional isomerization considering all possible reaction sites. This is also one of the first studies to investigate the effect of chirality on calculated rate constants. Results indicate that chirality is important when two chiral centers exist in the reactant. OOQOOH alternative isomerization rate constants are usually assigned in analogy to the isomerization of an alkylperoxy (RO2) radical which may introduce some uncertainty. To test the validity of using analogous rates, this study calculates the rate constants for selected alternative isomerization reactions. The effect of intramolecular hydrogen bonding in the calculated energies and rate constants for different reaction pathways is investigated. The result shows that alternative isomerization is a competing pathway only when it proceeds via a less strained transition state relative to the conventional isomerization transition state. A detailed analysis of the hydrogen bonding effect helped to identify cases where assigning rates in analogy may not be valid.

碩士
中國文化大學
化學系應用化學碩士班
102
The mechanism and kinetic for reaction of the iminovinylidene (HNCC) radical with the nitric oxide is investigated via considering the possible channels of the N and O atoms of NO attacking the N and C atoms of the HNCC based on high level ab initio molecular orbital in conjunction with variational TST and RRKM calculations. The species involved have been optimized at the B3LYP/6-311++G(3df,2p) level and their single−point energies are refined by the CCSD(T)/aug-cc-PVQZ//B3LYP/6-311++G(3df,2p) method. The calculated results of potential energy surfaces indicated that energetically the most favorable channel for the HNCC + NO reaction was predicted to be the formation of HNC+CNO (P8) product via the addition reaction of the C atom of HNCC radical and the N atom of NO with the head to head orientation. To rationalize the scenario of the calculated results, we also employ the Fukui functions and HSAB theory to seek for the possible explanation. In addition, the reaction rate constants were calculated using VariFlex code, and the results shows total rate coefficient, ktotal, at Ar pressure 760 torr can be represented with an equation: ktotal = 6.433×10-11 T 0.100 exp(0.275 kcal mol-1/RT) at T = 298-3000 K, in units of cm3 molecule-1 s-1.

Reactive chemicals are presented widely in the chemical and petrochemical process industry. Their chemical reactivity hazards have posed a significant challenge to the industries of manufacturing, storage and transportation. The accidents due to reactive chemicals have caused tremendous loss of properties and lives, and damages to the environment. In this research, three classes of reactive chemicals (unsaturated hydrocarbons, self-reacting chemicals, energetic materials) were evaluated through theoretical and experimental methods. Methylcyclopentadiene (MCP) and Hydroxylamine (HA) are selected as representatives of unsaturated hydrocarbons and self-reacting chemicals, respectively. Chemical reactivity of MCP, including isomerization, dimerization, and oxidation, is investigated by computational chemistry methods and empirical thermodynamic–energy correlation. Density functional and ab initio methods are used to search the initial thermal decomposition steps of HA, including unimolecular and bimolecular pathways. In addition, solvent effects are also examined using water cluster methods and Polarizable Continuum Models (PCM) for aqueous solution of HA. The thermal stability of a basic energetic material, Nitroethane, is investigated through both theoretical and experimental methods. Density functional methods are employed to explore the initial decomposition pathways, followed by developing detailed reaction networks. Experiments with a batch reactor and in situ GC are designed to analyze the distribution of reaction products and verify reaction mechanisms. Overall kinetic model is also built from calorimetric experiments using an Automated Pressure Tracking Adiabatic Calorimeter (APTAC). Finally, a general evaluation approach is developed for a wide range of reactive chemicals. An index of thermal risk is proposed as a preliminary risk assessment to screen reactive chemicals. Correlations are also developed between reactivity parameters, such as onset temperature, activation energy, and adiabatic time to maximum rate based on a limited number, 37 sets, of Differential Scanning Calorimeter (DSC) data. The research shows broad applications in developing reaction mechanisms at the molecular level. The methodology of reaction modeling in combination with molecular modeling can also be used to study other reactive chemical systems.

With an increased popularity for systems-based approaches in biology, a wide spectrum of techniques has been applied to the simulation and analysis of biochemical systems which involves uncertainty and stochasticity. It is particularly concerned with modelling and analysis of metabolic pathways, regulatory and signal transduction networks for understanding intra-cellular pathway behaviour. Typically, parameter estimation in ordinary differential equations(ODEs) models is used for this purpose when there is large number of molecules involved in the reaction system. However this approach is correct when the system is large enough to be deterministic in nature. But there are uncertainty involved in the system and the processes are stochastic in nature due to smaller population molecules participating in the pathway reactions. In this thesis the common theme is the study of uncertainties in the chemical kinetics of biochemical reaction systems associated with various intra-cellular pathways and channels. The study is at the mesoscale of the system, i.e., we study systems that do not have too few molecules disallowing any higher scale system level approximation nor too many where a non-stochastic (mesoscale) system approximation will be valid. In our first study we estimate the parameters in the mitogen activated protein kinase (MAPK) signal transduction pathway involved in the departure from the normal Epithelial Growth Factor(EGF) dose-dependency in prostate cancer cells. A model-based pathway analysis is performed. The pathway is mathematically modelled with 28 rate equations yielding those many ordinary differential equations(ODE) with kinetic rate constants that have been reported to take random values in the existing literature. This has led to us treating the ODE model of the pathways kinetics as a random differential equations(RDE) system in which the parameters are random variables. The most likely set of values of the kinetic rate constants obtained from fitting the RDE model into the experimental data is then used in a direct transcription based dynamic optimization method for computing the changes needed in these kinetic rate constant values for the restoration of the normal EGF dose response. It identifies the parameters, i.e., the kinetic rate constants in the RDE model, that are the most sensitive to the change in the EGF dose response behaviour in the PC3 prostate cancer cells. Biochemical pathways involving chemical kinetics equations in terms of low concen-trations of the model variables can be represented as chemical Langevin equations(CLE) as there is stochasticity involved in the processes. Most CLE systems come with the implicit constraint that the concentration state cannot be negative at any time over the sample path. Due to the inherent stiffness(especially in diffusion coefficient) of the CLE system, it has been difficult for numerical schemes to meet this positivity constraint during numerical simulations. Most available methods resort to heuristics by dropping selective noise terms from the original CLE inconsistent with the mesoscale physics involved in forming the CLE. Other methods take very small time steps thus making the simulation inefficient. In our second study we preserve positivity by using a physically consistent numerical scheme which is a modified form of fully stochastic α method for stiff stochastic differential equation. Ion channels are fundamental molecules in the nervous system that catalyse the flux of ions across the cell membrane. Single ion channel flux activity is comparable to the catalytic activity of single enzyme molecules. Saturating concentrations of substrate induce dynamic disorder in the kinetic rate processes of single enzyme molecules and consequently, develop correlative memory of the previous history of activities. Conversely, binding of substrate ion is known to alter the catalytic turnover of single ion channels. Here, we investigated the possible existence of dynamic disorder and molecular memory in single human TREK1 channel due to binding of substrate/agonist using the excised inside-out patch-clamp technique. Our results suggest that single hTREK1 channel behaves as a typical Michaelis-Menten enzyme molecule with a single high-affinity binding site for substrate K+ ion but with uncertainty in reaction rates.

With an increased popularity for systems-based approaches in biology, a wide spectrum of techniques has been applied to the simulation and analysis of biochemical systems which involves uncertainty and stochasticity. It is particularly concerned with modelling and analysis of metabolic pathways, regulatory and signal transduction networks for understanding intra-cellular pathway behaviour. Typically, parameter estimation in ordinary differential equations(ODEs) models is used for this purpose when there is large number of molecules involved in the reaction system. However this approach is correct when the system is large enough to be deterministic in nature. But there are uncertainty involved in the system and the processes are stochastic in nature due to smaller population molecules participating in the pathway reactions. In this thesis the common theme is the study of uncertainties in the chemical kinetics of biochemical reaction systems associated with various intra-cellular pathways and channels. The study is at the mesoscale of the system, i.e., we study systems that do not have too few molecules disallowing any higher scale system level approximation nor too many where a non-stochastic (mesoscale) system approximation will be valid. In our first study we estimate the parameters in the mitogen activated protein kinase (MAPK) signal transduction pathway involved in the departure from the normal Epithelial Growth Factor(EGF) dose-dependency in prostate cancer cells. A model-based pathway analysis is performed. The pathway is mathematically modelled with 28 rate equations yielding those many ordinary differential equations(ODE) with kinetic rate constants that have been reported to take random values in the existing literature. This has led to us treating the ODE model of the pathways kinetics as a random differential equations(RDE) system in which the parameters are random variables. The most likely set of values of the kinetic rate constants obtained from fitting the RDE model into the experimental data is then used in a direct transcription based dynamic optimization method for computing the changes needed in these kinetic rate constant values for the restoration of the normal EGF dose response. It identifies the parameters, i.e., the kinetic rate constants in the RDE model, that are the most sensitive to the change in the EGF dose response behaviour in the PC3 prostate cancer cells. Biochemical pathways involving chemical kinetics equations in terms of low concen-trations of the model variables can be represented as chemical Langevin equations(CLE) as there is stochasticity involved in the processes. Most CLE systems come with the implicit constraint that the concentration state cannot be negative at any time over the sample path. Due to the inherent stiffness(especially in diffusion coefficient) of the CLE system, it has been difficult for numerical schemes to meet this positivity constraint during numerical simulations. Most available methods resort to heuristics by dropping selective noise terms from the original CLE inconsistent with the mesoscale physics involved in forming the CLE. Other methods take very small time steps thus making the simulation inefficient. In our second study we preserve positivity by using a physically consistent numerical scheme which is a modified form of fully stochastic α method for stiff stochastic differential equation. Ion channels are fundamental molecules in the nervous system that catalyse the flux of ions across the cell membrane. Single ion channel flux activity is comparable to the catalytic activity of single enzyme molecules. Saturating concentrations of substrate induce dynamic disorder in the kinetic rate processes of single enzyme molecules and consequently, develop correlative memory of the previous history of activities. Conversely, binding of substrate ion is known to alter the catalytic turnover of single ion channels. Here, we investigated the possible existence of dynamic disorder and molecular memory in single human TREK1 channel due to binding of substrate/agonist using the excised inside-out patch-clamp technique. Our results suggest that single hTREK1 channel behaves as a typical Michaelis-Menten enzyme molecule with a single high-affinity binding site for substrate K+ ion but with uncertainty in reaction rates.

碩士
國立臺灣科技大學
化學工程系
91
The major gas-phase reaction pathways in the SiH4/GeH4—Si1-xGex— CVD reaction system has been investigated by molecular orbital theory calculations, together with a kinetic evaluation by transition state theory. The results indicate that primary pathway in the beginning is the decomposition of GeH4 to form GeH2 and H2 with an activation energy of 55 kcal/mol and a decomposition rate of 0.8 s-1 at 873 K, 100 times that of SiH4. Nevertheless, SiH2, an intermediate from SiH4, plays an important role in the subsequent reactions because of its much higher insertion reaction rates to form a series of intermediate SinGeH2(n+1)+2, which may be responsible for the experimental decrease of Ge/Si molar ratio in the films with increasing reaction resident time.

My thesis involves studying the pyrolysis/thermal decomposition of cyclohexane derivatives (important constituents of conventional transportation fuel). From the literature as well as the composition analysis of two fuels (JP-7(eq) and RP-1) performed in our lab using GC-MS, we found that cyclohexane derivatives can be categorized into different types: single side-chain alkylcyclohexane; multiple side-chain alkylcyclohexane, and decalin (two fused cyclohexane ring). We have taken iso-propylcyclohexane as a member of single side-chain alkylcyclohexane and 1,3,5-trimethylcyclohexane as a member of multiple side-chain alkylcyclohexane. We have carried out a detailed theoretical study on the various possible reactions of both molecules and associated intermediates/radicals involved in pyrolysis. State-of-the-art quantum chemical calculations have allowed us to probe the transition states for all the reactions and calculate the high-pressure rate constants. We have also carried out experimental investigations using a single pulse shock tube for both molecules. Concentrations of all the major and minor products have been measured using GC-FID and GC-MS. Experimental measurements have been used to validate the kinetic mechanism proposed in the theoretical study. We have used Chemkin for kinetic simulation. We have proposed detailed kinetic models for the pyrolysis of iso-propylcyclohexane as well as 1,3,5-trimethylcyclohexane. For decalin, we have done only a detailed theoretical investigation of its thermal decomposition and proposed a detailed kinetics mechanism of its decomposition based on our calculations. We have also calculated high-pressure limit rate parameters for all the elementary reactions. Other important part of my thesis involves the computational investigation of C2+C2 reaction. The addition of these pure carbon molecules is very important in combustion. Our calculation shows that the C2+C2 reaction leads to C3+C, which is not a barrier-less reaction, occurring via C4. We have calculated pressure-dependent rate parameters to determine the temperature and pressure condition in which C2+C2 leads to C3+C. We also found that spin states of C2 play a key role in this reaction.

Over one million amputees are living in the United States with major lower limb loss (Ziegler-Graham et al. 2008). Lower limb amputation leads to the functional loss of the ankle plantar flexor muscles, which are important contributors to body support, forward propulsion, and leg swing initiation during walking (Neptune et al. 2001; Liu et al. 2006). Effective prosthetic component design is essential for successful rehabilitation of amputees to return to an active lifestyle by partially replacing the functional role of the ankle muscles. The series of experimental and computer simulation studies presented in this research showed that design characteristics of energy storage and return prosthetic ankles, specifically the elastic stiffness, significantly influence residual and intact leg ground reaction forces, knee joint moments, and muscle activity, thus affecting muscle output. These findings highlight the importance of proper prosthetic foot stiffness prescription for amputees to assure effective rehabilitation outcomes. The research also showed that the ankle muscles serve to stabilize the body during turning the center of mass. When amputees turn while supported by their prosthetic components, they rely more on gravity to redirect the center of mass than active muscle generation. This mechanism increases the risks of falling and identifies a need for prosthetic components and rehabilitation focused on increasing amputee stability during turning. A proper understanding of the effects of prosthetic components on amputee walking mechanics is critical to decreasing complications and risks that are prevalent among lower-limb amputees. The presented research is an important step towards reaching this goal.
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The Diels-Alder reaction was discovered in 1928 and has become the most efficient and practical method for the synthesis of six-membered carbocyclic and heterocyclic rings. This thesis comprises three chapters of results and discussion with the Diels-Alder reaction as a theme. Chapter 2 details an investigation of endo:exo selectivity in the Diels-Alder reactions of 1,3-butadiene. Chapter 3 explores aspects of the intramolecular Diels-Alder reactions of some substituted 1,3,8-nonatrienes, and Chapter 4 describes the domino Diels-Alder reactions of 1,4-diiodo-1,3-butadiene. The Diels-Alder reaction is powerful, general, and widely used in chemical synthesis, and it is well known that many Diels-Alder reactions exhibit endo selectivity, in accord with Alder’s empirical rule. The origins of endo:exo selectivity in the Diels-Alder reaction, however, are not completely understood and there is a dearth of experimental evidence concerning the Diels-Alder reactions of the archetypal 1,3-diene, 1,3- butadiene. Chapter 2 describes a study of the Diels-Alder reactions of an isotopically labelled 1,3-butadiene with a range of simple dienophiles, allowing the endo:exo selectivities of these important reactions to be determined for the first time. The experimental data shed light on the origins of endo:exo selectivity in the Diels-Alder reaction and will serve as an important reference for future computational investigations in this area. The intramolecular Diels-Alder reaction shares many of the virtues of its intermolecular counterpart, however its use in chemical synthesis is limited because intramolecular Diels-Alder reactivity and stereoselectivity are often governed by subtle factors, and can be very difficult to predict. As part of a comprehensive experimental and computational collaboration, Chapter 3 describes an investigation of the heat and Lewis acid promoted intramolecular Diels-Alder reactions of some ether tethered 1,3,8-nonatrienes. Also presented are the results of a rate study and a kinetic isotope effect study involving the intramolecular Diels-Alder reactions of some 1,3,8-nonatrienes. The experimental data are analysed and compared with predicted stereoselectivities, activation barriers and kinetic isotope effects obtained from computational modelling. Increased efficiency in chemical synthesis conserves resources, reduces waste, and saves time and money. Domino reactions are particularly efficient processes, which can generate complex products from simple reactants. Chapter 4 describes an investigation of the domino Diels-Alder reactions of (1E,3E)-1,4-diiodo-1,3-butadiene with maleimide dienophiles, through which a family of bicyclo[2.2.2]oct-2-ene derivatives are produced in one high yielding and stereoselective synthetic step.

abstract: This work is concerned with the study and numerical solution of large reaction diffusion systems with applications to the simulation of degradation effects in solar cells. A discussion of the basics of solar cells including the function of solar cells, the degradation of energy efficiency that happens over time, defects that affect solar cell efficiency and specific defects that can be modeled with a reaction diffusion system are included. Also included is a simple model equation of a solar cell. The basics of stoichiometry theory, how it applies to kinetic reaction systems, and some conservation properties are introduced. A model that considers the migration of defects in addition to the reaction processes is considered. A discussion of asymptotics and how it relates to the numerical simulation of the lifetime of solar cells is included. A reduced solution is considered and a presentation of a numerical comparison of the reduced solution with the full solution on a simple test problem is included. Operator splitting techniques are introduced and discussed. Asymptotically preserving schemes combine asymptotics and operator splitting to use reasonable time steps. A presentation of a realistic example of this study applied to solar cells follows.
Dissertation/Thesis
Doctoral Dissertation Applied Mathematics 2020

abstract: The heat and mass transfer phenomena in micro-scale for the mass transfer phenomena on drug in cylindrical matrix system, the simulation of oxygen/drug diffusion in a three dimensional capillary network, and a reduced chemical kinetic modeling of gas turbine combustion for Jet propellant-10 have been studied numerically. For the numerical analysis of the mass transfer phenomena on drug in cylindrical matrix system, the governing equations are derived from the cylindrical matrix systems, Krogh cylinder model, which modeling system is comprised of a capillary to a surrounding cylinder tissue along with the arterial distance to veins. ADI (Alternative Direction Implicit) scheme and Thomas algorithm are applied to solve the nonlinear partial differential equations (PDEs). This study shows that the important factors which have an effect on the drug penetration depth to the tissue are the mass diffusivity and the consumption of relevant species during the time allowed for diffusion to the brain tissue. Also, a computational fluid dynamics (CFD) model has been developed to simulate the blood flow and oxygen/drug diffusion in a three dimensional capillary network, which are satisfied in the physiological range of a typical capillary. A three dimensional geometry has been constructed to replicate the one studied by Secomb et al. (2000), and the computational framework features a non-Newtonian viscosity model for blood, the oxygen transport model including in oxygen-hemoglobin dissociation and wall flux due to tissue absorption, as well as an ability to study the diffusion of drugs and other materials in the capillary streams. Finally, a chemical kinetic mechanism of JP-10 has been compiled and validated for a wide range of combustion regimes, covering pressures of 1atm to 40atm with temperature ranges of 1,200 K - 1,700 K, which is being studied as a possible Jet propellant for the Pulse Detonation Engine (PDE) and other high-speed flight applications such as hypersonic missiles. The comprehensive skeletal mechanism consists of 58 species and 315 reactions including in CPD, Benzene formation process by the theory for polycyclic aromatic hydrocarbons (PAH) and soot formation process on the constant volume combustor, premixed flame characteristics.
Dissertation/Thesis
Ph.D. Aerospace Engineering 2012

Thermodynamic and kinetic analysis of the ligand substitution reactions of different heterometallic Ru(II)-Pt(II) complexes with a series of bio-relevant thiourea nucleophiles of different steric demands and ionic nucleophiles have been investigated as a function of concentration and temperature using UV/visible and stopped-flow spectrophotometric techniques. To achieve this, five different sets of complexes involving mono di and multinuclear homo and heterometallic complexes with tridentate N-donor ligands of different linker ligands were synthesized and characterized by various spectroscopic methods. The substitution reactions of the chloride complexes were studied in methanol in the presence of 0.02 M LiCf3SO3 adjusted with LiCl to prevent possible solvolysis. The aqua complexes were studied in acidic aqueous medium at pH 2.0. All reactions were investigated under pseudo first-order conditions. Density functional theory (DFT) calculations were used to aid further interpretations and understandings of the experimental results. Substitution reactivity of heterometallic Ru(II)-Pt(II) and Co(II)-Pt(II) complexes bridged by tetra-2-pyridyl-1,4-pyrazine (tppz) ligand was investigated for the first time. The reactions proceeded via two steps. The pseudo first-order rate constants, kobs(1st and 2nd) for the substitution of the chloride ligand(s) from the Pt(II) complexes and subsequent displacement of the linker. The dechelation step was confirmed by 1H NMR and 195Pt NMR studies. Incorporation of Ru(tppz) moiety increases the substitution reactivity and is ascribed to the increased π-back donation from the tppz ligand which increases the electrophilicity of the metal centre, overall charge and the global electrophilicity index of the complex. However, when changed the second metal centre from a Ru(II) to a Co(II), the rate of substitution decreased by a factor of four due to the weaker π- backbonding from Co(II). The substitution reactivity of another set of heterometallic Ru(II)-Pt(II) complexes with a semi-rigid linker, 4’-pyridyl-2,2’:6’,2”-terpyridine (qpy) showed that replacing the cis pyridyl group by a (tpy)Ru(qpy) moiety lowers the energy of anti-bonding LUMO (π*) orbitals and increases the metal-metal interactions and electronic transition within the complex whereby enhancing the reactivity of Pt(II) centre. However, when two Pt(II) moieties are linked to a (qpy)Ru(qpy), the orthogonal geometry at the Ru(II) metal centre prevents the extended π-electron density to flow through the three metal centres. The kinetic results obtained were supported by pKa and 195Pt NMR studies. Substitution reactions of the mononuclear Pt(II) complexes revealed that the polyethylene glycoxy pendent units act as a σ-donors including the lone pair electrons on the first oxygen atom thereby decreasing the reactivity of the parent Pt(II) terpyridine complex. However, this σ-donation towards the terpyridine moiety was found to be effective only up to one unit of the ethylene glycoxy pendant, beyond which the reactivity was sterically controlled. The dinuclear Pt(II) complexes bridged by polyehtyleneglycol ether units show that the reactivity of the complexes depend on the Pt···Pt distance and the steric hindrance at the Pt(II) centre. The substitution reactivity of heterometallic Ru(II)-Pt(II) complexes bridged by the same polyehtyleneglycol ether units indicate that the presence of Ru(tpy)2 moiety influences the structural geometry of the complex system which in turn controls the reactivity of the Pt(II) centre. This is further driven by the entrapment effect of the nucleophile due to the V-shape geometry adopted by the heterometallic complexes. In all cases the reactivity was also controlled by steric and electronic effects. However, when two metal centres are bridged by a flexible non-aromatic linker, the electronic transitions and the metal-metal interactions were found to be minor, especially for the longer linkers. The 1H and 195Pt NMR spectroscopic techniques were used to further understand the observed substitution kinetics and to confirm the degradation of the bridging ligand from the metal centre(s). In all cases, the negative activation entropies obtained support the associative mode of substitution This investigation reveals that the length and the nature of the bridging linker plays an important role in controlling the reactivity of the heterometallic complexes. It is envisaged that the findings of this project would offer a significant contribution to the pharmacological design of effective anticancer drugs.
Ph.D. University of KwaZulu-Natal, Pietermaritzburg 2013.

Although Cu-SSZ-13 zeolites are used commercially in diesel engine exhaust after-treatment for abatement of toxic NO_x pollutants via selective catalytic reduction (SCR) with NH₃, molecular details of its active centers and mechanistic details of the redox reactions they catalyze, specifically of the Cu(I) to Cu(II) oxidation half-reaction, are not well understood. A detailed understanding of the SCR reaction mechanism and nature of the Cu active site would provide insight into their catalytic performance and guidance on synthesizing materials with improved low temperature (< 473 K) reactivity and stability against deactivation (e.g. hydrothermal, sulfur oxides). We use computational, titration, spectroscopic, and kinetic techniques to elucidate (1) the presence of two types of Cu²⁺ ions in Cu-SSZ-13 materials, (2) molecular details on how these Cu cations, facilitated by NH₃ solvation, undergo a reduction-oxidation catalytic cycle, and (3) that sulfur oxides poison the two different types of Cu²⁺ ions to different extents at via different mechanisms.

Copper was exchanged onto H-SSZ-13 samples with different Si:Al ratios (4.5, 15, and 25) via liquid-phase ion exchange using Cu(NO₃)₂ as the precursor. The speciation of copper started from the most stable Cu²⁺ coordinated to two anionic sites on the zeolite framework to [CuOH]⁺ coordinated to only one anionic site on the zeolite framework with increasing Cu:Al ratios. The number of Cu²⁺ and [CuOH]⁺ sites was quantified by selective NH₃ titration of the number of residual Brønsted acid sites after Cu exchange, and by quantification of Brønsted acidic Si(OH)Al and CuOH stretching vibrations from IR spectra. Cu-SSZ-13 with similar Cu densities and anionic framework site densities exhibit similar standard SCR rates, apparent activation energies, and orders regardless of the fraction of Z₂Cu and ZCuOH sites, indicating that both sites are equally active within measurable error for SCR.

The standard SCR reaction uses O₂ as the oxidant (4NH₃ + 4NO + O₂ -> 6H₂O + 4N₂) and involves a Cu(I)/Cu(II) redox cycle, with Cu(II) reduction mediated by NO and NH₃, and Cu(I) oxidation mediated by NO and O₂. In contrast, the fast SCR reaction (4NH₃ + 2NO + 2NO₂ -> 6H₂O + 4N₂) uses NO₂ as the oxidant. Low temperature (437 K) standard SCR reaction kinetics over Cu-SSZ-13 zeolites depend on the spatial density and distribution of Cu ions, varied by changing the Cu:Al and Si:Al ratio. Facilitated by NH₃ solvation, mobile Cu(I) complexes can dimerize with other Cu(I) complexes within diffusion distances to activate O₂, as demonstrated through X-ray absorption spectroscopy and density functional theory calculations. Monte Carlo simulations are used to define average Cu-Cu distances. In contrast with O₂-assisted oxidation reactions, NO₂ oxidizes single Cu(I) complexes with similar kinetics among samples of varying Cu spatial density. These findings demonstrate that low temperature standard SCR is dependent on Cu spatial density and requires NH₃ solvation to mobilize Cu(I) sites to activate O₂, while in contrast fast SCR uses NO₂ to oxidize single Cu(I) sites.

We also studied the effect of sulfur oxides, a common poison in diesel exhaust, on Cu-SSZ-13 zeolites. Model Cu-SSZ-13 samples exposed to dry SO₂ and O₂ streams at 473 and 673 K. These Cu-SSZ-13 zeolites were synthesized and characterized to contain distinct Cu active site types, predominantly either divalent Cu²⁺ ions exchanged at proximal framework Al sites (Z₂Cu), or monovalent CuOH+ complexes exchanged at isolated framework Al sites (ZCuOH). On the model Z₂Cu sample, SCR turnover rates (473 K, per Cu) catalyst decreased linearly with increasing S content to undetectable values at equimolar S:Cu molar ratios, while apparent activation energies remained constant at ~65 kJ mol^-1, consistent with poisoning of each Z₂Cu site with one SO₂-derived intermediate. On the model ZCuOH sample, SCR turnover rates also decreased linearly with increasing S content, yet apparent activation energies decreased monotonically from ~50 to ~10 kJ mol^-1, suggesting that multiple phenomena are responsible for the observed poisoning behavior and consistent with findings that SO₂ exposure led to additional storage of SO₂-derived intermediates on non-Cu surface sites. Changes to Cu²⁺ charge transfer features in UV-Visible spectra were more pronounced for SO₂-poisoned ZCuOH than Z₂Cu sites, while X-ray diffraction and micropore volume measurements show evidence of partial occlusion of microporous voids by SO₂-derived deposits, suggesting that deactivation may not only reflect Cu site poisoning. Density functional theory calculations are used to identify the structures and binding energies of different SO₂-derived intermediates at Z₂Cu and ZCuOH sites. It is found that bisulfates are particularly low in energy, and residual Brønsted protons are liberated as these bisulfates are formed. These findings indicate that Z₂Cu sites are more resistant to SO₂ poisoning than ZCuOH sites, and are easier to regenerate once poisoned.

Kinetic studies determining the second order rate constants for the monoepoxidation of cyclic dienes, 1,3-cyclohexadiene and 1,3-cyclooctadiene, and the epoxidation of cis-/trans-2-hexenes by dimethyldioxirane (DMDO) were carried out using UV methodology. Consistent with published results, the kinetics of cis-/trans-2-hexenes by DMDO showed greater reactivity of the cis-isomer compared to that of the trans-compound. Molecular modeling studies for the epoxidation of a series of cis-/trans-alkenes, by DMDO were carried out using the DFT approach. The mechanism of epoxidation by DMDO was modeled by determining the transition state geometry and calculating the electronic activation energies and relative reactivities. The calculations were consistent with a concerted, electrophilic, exothermic process with a spiro-transition state for all cases. Kinetic studies for the monoepoxidation of the cyclic dienes showed a greater reactivity for 1,3-cyclohexadiene compared to that for 1,3-cyclooctadiene. The DFT method was employed to successfully model the transition state for the monoepoxidation of the cyclic dienes by DMDO and successfully predict the relative reactivities. Student misconceptions, at the high school and/or middle school level involving energy changes and chemical reactions have been prevalently noted in literature (by ACS and AAAS). Two examples of these misconceptions are: 1) heat is always needed to initiate a chemical reaction and 2) all chemical reactions create or destroy energy. In order to address these types of misconceptions, an educational module detailing the influence of energy changes on chemical reactions has been developed in conjunction with the Bio-bus program for middle and high school students. Visual aids and hands-on activities were developed in the module to potentially help students overcome/deal with the common misconceptions. Surveys were designed to access the situations (determine the extent of the misconceptions) and the effectiveness of the educational module, before and immediately after the module and one-month later to determine retention. The educational module has been presented to approximately 100 high school students from underrepresented communities. Pre-survey data confirmed the presence of the common misconceptions reported in the literature. Data from the post-survey indicated the new instructional module enhanced the student’s interest of science and expanded their content knowledge and laboratory skills. The post-survey data (immediately following the module) showed a significant difference in two out of five misconceptions when compared to the pre-survey data. However, this significance decreased when the 1-month post-survey data were compared to the pre-survey data.

Selective catalytic reduction (SCR) of NO_x using NH₃ as a reductant (4NH₃+ 4NO + O₂ 6H₂O + 4N₂) over Cu-SSZ-13 zeolites is a commercial technology used to meet emissions targets in lean-burn and diesel engine exhaust. Optimization of catalyst design parameters to improve catalyst reactivity and stability against deactivation (hydrothermal and sulfur poisoning) necessitates detailed molecular level understanding of structurally different active Cu sites and the reaction mechanism. With the help of synthetic, titrimetric, spectroscopic, kinetic and computational techniques, we established new molecular level details regarding 1) active Cu site speciation in monomeric and dimeric complexes in Cu-SSZ-13, 2) elementary steps in the catalytic reaction mechanism, 3) and deactivation mechanisms upon hydrothermal treatment and sulfur poisoning.

We have demonstrated that Cu in Cu-SSZ-13 speciates as two distinct isolated sites, nominally divalent Cu^II and monovalent [Cu^II(OH)]⁺ complexes exchanged at paired Al and isolated Al sites, respectively. This Cu site model accurately described a wide range of zeolite chemical composition, as evidenced by spectroscopic (Infrared and X-ray absorption) and titrimetric characterization of Cu sites under ex situ conditions and in situ and operando SCR reaction conditions. Monovalent [Cu^II(OH)]⁺ complexes have been further found to condense to form multinuclear Cu-oxo complexes upon high temperature oxidative treatment, which have been characterized using UV-visible spectroscopy, CO-temperature programmed reduction and dry NO oxidation as a probe reaction. Structurally different isolated Cu sites have different susceptibilities to H₂ and He reductions, but are similarly susceptible to NO+NH₃ reduction and have been found to catalyze NO_x SCR reaction at similar turnover rates (per Cu^II; 473 K) via a Cu^II/Cu^I redox cycle, as their structurally different identities are masked by NH₃ solvation during reaction.

Molecular level insights on the low temperature Cu^II/Cu^I redox mechanism have been obtained using experiments performed in situand in operando coupled withtheory. Evidence has been provided to show that the Cu^II to Cu^I reduction half-cycle involves single-site Cu reduction of isolated Cu^II sites with NO+NH₃, which is independent of Cu spatial density. In contrast, the Cu^I to Cu^II oxidation half-cycle involves dual-site Cu oxidation with O₂ to form dimeric Cu-oxo complexes, which is dependent on Cu spatial density. Such dual-site oxidation during the SCR Cu^II/Cu^I redox cycle requires two Cu^I(NH₃)₂sites, which is enabled by NH₃solvation that confers mobility to isolated Cu^I sites and allows reactions between two Cu^I(NH₃)₂ species and O₂. As a result, standard SCR rates depend on Cu proximity in Cu-SSZ-13 zeolites when Cu^I oxidation steps are kinetically relevant. Additional unresolved pieces of mechanism have been investigated, such as the reactivity of Cu dimers, the types of reaction intermediates involved, and the debated role of Brønsted acid sites in the SCR cycle, to postulate a detailed reaction mechanism. A strategy has been discussed to operate either in oxidation or reduction-limited kinetic regimes, to extract oxidation and reduction rate constants, and better interpret the kinetic differences among Cu-SSZ-13 catalysts.

The stability of active Cu sites upon sulfur oxide poisoning has been assessed by exposing model Cu-zeolite samples to dry SO₂ and O₂ streams at 473 and 673 K, and then analyzing the surface intermediates formed via spectroscopic and kinetic assessments. Model Cu-SSZ-13 zeolites were synthesized to contain distinct Cu active site types, predominantly either divalent Cu^II ions exchanged at proximal framework Al (Z₂Cu), or monovalent [Cu^IIOH]⁺ complexes exchanged at isolated framework Al (ZCuOH). SCR turnover rates (473 K, per Cu) decreased linearly with increasing S content to undetectable values at equimolar S:Cu ratios, consistent with poisoning of each Cu site with one SO₂-derived intermediate. Cu and S K-edge X-ray absorption spectroscopy and density functional theory calculations were used to identify the structures and binding energies of different SO₂-derived intermediates at Z₂Cu and ZCuOH sites, revealing that bisulfates are particularly low in energy, and residual Brønsted protons are liberated at Z₂Cu sites as bisulfates are formed. Molecular dynamics simulations also show that Cu sites bound to one HSO₄^- are immobile, but become liberated from the framework and more mobile when bound to two HSO₄^-. These findings indicate that Z₂Cu sites are more resistant to SO₂poisoning than ZCuOH sites, and are easier to regenerate once poisoned.

The stability of active Cu sites on various small-pore Cu-zeolites during hydrothermal deactivation (high temperature steaming conditions) has also been assessed by probing the structural and kinetic changes to active Cu sites. Three small-pore, eight-membered ring (8-MR) zeolites of different cage-based topology (CHA, AEI, RTH) have been investigated. With the help of UV-visible spectroscopy to probe the Cu structure, in conjunction with measuring differential reaction kinetics before and after subsequent treatments, it has been suggested that the RTH framework imposes internal transport restrictions, effectively functioning as a 1-D framework during SCR catalysis. Hydrothermal aging of Cu-RTH results in complete deactivation and undetectable SCR rates, despite no changes in long-range structure or micropore volume after hydrothermal aging treatments and subsequent SCR exposure, highlighting beneficial properties conferred by double six-membered ring (D6R) composite building units. Exposure aging conditions and SCR reactants resulted in deleterious structural changes to Cu sites, likely reflecting the formation of inactive copper-aluminate domains. Therefore, the viability of Cu-zeolites for practical low temperature NO_x SCR catalysis cannot be inferred solely from assessments of framework structural integrity after aging treatments, but also require Cu active site and kinetic characterization after aged zeolites are exposed to low temperature SCR conditions.

Droplets as precursor are extensively applied in diverse fields of science and engineering. Various contributions are provided previously towards analysis of single phase and multi-phase droplets of single and multiple components. This thesis describes modelling of multi-phase (nano fluid) droplet vaporization. The evaporation of liquid phase along with migration of dispersed particles in two-dimensional plane within droplet is detailed using the governing transport equations along with the appropriate boundary and interface conditions. The evaporation model is incorporated with aggregate kinetics to study agglomeration among nano silica particles in base water. Agglomeration model based on population balance approach is used to track down the aggregation kinetics of nano particles in the droplet. With the simulated model it is able to predict different types of final structure of the aggregates formed as observed in experimental results available in literature. High spatial resolution in terms of agglomeration dynamics is achieved using current model. Comparison based study of aggregation dynamics is done by heating droplet in convective environment as well as with radiations and using different combination of heating and physical parameters. The effect of internal flow field is also analysed with comparative study using levitation and without levitation individually. For levitation, droplet is stabilized in an acoustic standing wave. It is also attempted to study the transformation of cerium nitrate to ceria in droplets when heated under different environmental conditions. Reaction kinetics based on modified rate equation is modelled along with vaporization in aqueous cerium nitrate droplet. The thermo physical changes within the droplet along with dissociation reaction is analysed under different modes of heating. The chemical conversion of cerium nitrate to ceria during the process is predicted using Kramers' reaction velocity equation in a modified form. The model is able to explain the kinetics behind formation of ceria within droplet at low temperatures. Transformation of chemical species is observed to be influenced by temperature and configuration of the system. Reaction based model along with CFD (computational fluid dynamics) simulation within the droplet is able to determine the rate of chemical dissociation of species and predict formation of ceria within the droplet. The prediction shows good agreement with experimental data which are obtained from literature.

Droplets as precursor are extensively applied in diverse fields of science and engineering. Various contributions are provided previously towards analysis of single phase and multi-phase droplets of single and multiple components. This thesis describes modelling of multi-phase (nano fluid) droplet vaporization. The evaporation of liquid phase along with migration of dispersed particles in two-dimensional plane within droplet is detailed using the governing transport equations along with the appropriate boundary and interface conditions. The evaporation model is incorporated with aggregate kinetics to study agglomeration among nano silica particles in base water. Agglomeration model based on population balance approach is used to track down the aggregation kinetics of nano particles in the droplet. With the simulated model it is able to predict different types of final structure of the aggregates formed as observed in experimental results available in literature. High spatial resolution in terms of agglomeration dynamics is achieved using current model. Comparison based study of aggregation dynamics is done by heating droplet in convective environment as well as with radiations and using different combination of heating and physical parameters. The effect of internal flow field is also analysed with comparative study using levitation and without levitation individually. For levitation, droplet is stabilized in an acoustic standing wave. It is also attempted to study the transformation of cerium nitrate to ceria in droplets when heated under different environmental conditions. Reaction kinetics based on modified rate equation is modelled along with vaporization in aqueous cerium nitrate droplet. The thermo physical changes within the droplet along with dissociation reaction is analysed under different modes of heating. The chemical conversion of cerium nitrate to ceria during the process is predicted using Kramers' reaction velocity equation in a modified form. The model is able to explain the kinetics behind formation of ceria within droplet at low temperatures. Transformation of chemical species is observed to be influenced by temperature and configuration of the system. Reaction based model along with CFD (computational fluid dynamics) simulation within the droplet is able to determine the rate of chemical dissociation of species and predict formation of ceria within the droplet. The prediction shows good agreement with experimental data which are obtained from literature.