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Enzymes are biological catalysts which greatly accelerate the rates of chemical reactions, oftentimes by many orders of magnitude over the uncatalyzed reaction. The remarkable catalytic rate enhancement afforded by enzymes derives ultimately from the structure and chemical properties of the enzyme active sites, which allow enzymes to selectively bind to their substrates and to stabilize high energy chemical species and unstable intermediates along the reaction coordinate. To enhance their catalytic ability, many enzymes have also evolved to require coenzymes for optimal activity. These coenzymes often provide chemical functionality and reactivity that are not accessible by the twenty canonical amino acids and, hence, coenzymes serve to greatly enhance the diversity of chemical reactions that can be mediated by enzymes. The work described in this dissertation focuses on mechanistic studies of two enzymes that use common coenzymes in unusual ways. In the first section of this work, studies will focus on the type II isopentenyl diphosphate:dimethylallyl diphosphate isomerase (IDI-2), an essential enzyme in isoprenoid biosynthesis that employs a flavin mononucleotide (FMN) coenzyme for catalysis. In most biological systems, flavin coenzymes mediate electron transfer reactions. However, the IDI-2 catalyzed reaction involves no net redox change, raising questions as to the role of the flavin in the chemical mechanism. The chemical mechanism of IDI-2 will be interrogated with a combination of spectroscopic studies and biochemical techniques. Our studies suggest that the flavin coenzyme of IDI-2 may employ a novel mode of flavin-dependent catalysis involving acid/base chemistry. In the second section of this dissertation, attention will be focused on elucidating the chemical mechanism of 1-aminocyclopropane-1-carboxylate deaminase (ACCD), an enzyme that plays a role in regulating the production of the potent plant hormone, ethylene. ACCD is a pyridoxal-5ʹ-phosphate (PLP)-dependent enzyme that catalyzes a C-C bond cleavage event that is unique among the catalytic cycles of PLP-dependent enzymes. Altogether, our mechanistic studies of IDI-2 and ACCD help to illustrate the catalytic diversity of common coenzymes, and demonstrate that some enzymes have evolved to exploit readily available coenzymes for atypical reactions. / text

Understanding chemical reactions is crucial in learning chemistry at all educational levels. Nevertheless, research in science education has revealed that many students struggle to understand chemical processes. Improving teaching and learning about chemical reactions demands that we develop a clearer understanding of student reasoning in this area and of how this reasoning evolves with training in the discipline. Thus, we have carried out a qualitative study using semi-structured interviews as the main data collection tool to explore students reasoning about reaction mechanism and causality. The participants of this study included students at different levels of training in chemistry: general chemistry students (n=22), organic chemistry students (n=16), first year graduate students (n=13) and Ph.D. candidates (n=14). We identified major conceptual modes along critical dimensions of analysis, and illustrated common ways of reasoning using typical cases. Main findings indicate that although significant progress is observed in student reasoning in some areas, major conceptual difficulties seem to persist even at the more advanced educational levels. In addition, our findings suggest that students struggle to integrate important concepts when thinking about mechanism and causality in chemical reactions. The results of our study are relevant to chemistry educators interested in learning progressions, assessment, and conceptual development.

Choline oxidase catalyzes the four-electron oxidation of choline to glycine betaine, a limited number of compounds that accumulate to high levels in cytoplasm to prevent dehydration and plasmolysis in adverse hyperosmotic environments. With this respect, the study of choline oxidase has potential for the development of therapeutic agents that inhibit the biosynthesis of glycine betaine, thereby rendering pathogenic bacteria susceptible to either conventional treatments or the immune system. In this study, the highly GC rich codA gene encoding for choline oxidase was cloned, expressed. The resulting enzyme was purified to high levels, allowing for detailed biochemical, mechanistic and structural characterizations. A chemical mechanism for the reaction catalyzed by choline oxidase was established by using kinetic isotope effects and viscosity effects as probes, in which the choline hydroxyl proton is not in flight in the transition state for CH bond cleavage. Furthermore, these experiments indicated that chemical steps of flavin reduction by choline and betaine aldehyde are rate limiting for the overall turnover of the enzyme. Further mechanistic characterization clearly suggested a hydride transfer mechanism that is fully quantum mechanical. The structure of choline oxidase was resolved at 1.86 Å resolution in collaboration with the group of Dr. Allen O. Orville, at the Georgia Institute of Technology, providing a structural framework that is consistent with the mechanistic studies. The results of these studies will be presented and discussed in the context of the Glucose-Methanol-Choline oxidoreductase enzyme superfamily, of which choline oxidase is a member. Previous structural and mechanistic studies of alcohol- and aldehyde-oxidizing enzymes with different cofactors, as well as the biotechnological and biomedical relevance of choline oxidase are presented in Chapter 1. Chapter 3-8 illustrate my studies on choline oxidase, including cloning, expression, purification and preliminary characterizations (Chapter 3), spectroscopic and steady state kinetics (Chapter 4), the determination of the chemical mechanism for alcohol oxidation and the investigation of the involvement of quantum mechanical tunneling (Chapter 5 and 6), the study of aldehyde oxidation (Chapter 7), and the structural determination of choline oxidase by x-ray crystallography (Chapter 8). Chapter 9 presents a general discussion of the data presented.

Choline oxidase catalyzes the oxidation of choline to glycine betaine. This reaction is of considerable medical and biotechnological applications, because the accumulation of glycine betaine in the cytoplasm of many plants and human pathogens enables them to counteract hyperosmotic environments. In this respect, the study of choline oxidase has potential for the development of a therapeutic agent that can specifically inhibit the formation of glycine betaine, and therefore render pathogens more susceptible to conventional treatment. The study of choline oxidase has also potential for the improvement of the stress resistance of plant by introducing an efficient biosynthetic pathway for glycine betaine in genetically engineered economically relevant crop plant. In this study, codA gene encoding for choline oxidase was cloned. The cloned gene was then used to express and purify the wild-type enzyme as well as to prepare selected mutant forms of choline oxidase. In all cases, the resulting enzymes were purified to high levels, allowing for detailed characterizations. The biophysical and biochemical analyses of choline oxidase variants in which the positively charged residue close to the flavin N(1) locus (His466) was removed (H466A) or reversed (H466D) suggest that in choline oxidase, His466 modulates the electrophilicity of the bound flavin and the polarity of the active site, and contributes to the flavinylation process of the covalently bound FAD as well as to the stabilization of the negative charges in the active site. Biochemical, structural, and mechanistic relevant properties of selected flavoproteins with special attention to flavoprotein oxidases, as well as the biotechnological and medical relevance of choline oxidase, are presented in Chapter I. Chapter II summarizes all the experimental techniques used in this study. Chapter III-VII illustrate my studies on choline oxidase, including cloning, expression, purification and preliminary characterizations (Chapter III), spectroscopic and steady state kinetics (Chapter IV), the catalytic roles of His466 and the effects of reversing the protein positive charge close to the flavin N(1) locus (Chapter V and VI), and the roles of His310 with a special attention to its involvement in a proton-transfer network (Chapter VII). Chapter VIII presents a general discussion of the data presented.

The enzymatic oxidation of choline to glycine betaine is of interest because organisms accumulate glycine betaine intracellularly in response to stress conditions, as such it is of potential interest for the genetic engineering of crops that do not naturally possess efficient pathways for the synthesis of glycine betaine, and for the potential development of drugs that target the glycine betaine biosynthetic pathway in human pathogens. To date, one of the best characterized enzymes belonging to this pathway is the flavin-dependent choline oxidase from Arthrobacter globiformis. In this enzyme, choline oxidation proceeds through two reductive half-reactions and two oxidative half-reactions. In each of the reductive half-reactions the FAD cofactor is reduced to the anionic hydroquinone form (2 e- reduced) which is followed by an oxidative half-reaction where the reduced FAD cofactor is reoxidized by molecular oxygen with formation and release of hydrogen peroxide. In this dissertation the roles of selected residues, namely histidine at position 310, valine at position 464 and serine at position 101, that do not directly participate in catalysis in the reaction catalyzed by choline oxidase have been elucidated. The effects on the overall reaction kinetics of these residues in the protein matrix were investigated by a combination of steady state kinetics, rapid kinetics, pH, mutagenesis, substrate deuterium and solvent isotope effects, viscosity effects as well as X-ray crystallography. A comparison of the kinetic data obtained for the variant enzymes to previous data obtained for wild-type choline oxidase are consistent with the valine residue at position 464 being important for the oxidative half-reaction as well as the positioning of the catalytic groups in the active site of the enzyme. The kinetic data obtained for the serine at position 101 shows that serine 101 is important for both the reductive and oxidative half-reactions. Finally, the kinetic data for histidine at position 310 suggest that this residue is essential for both the reductive and oxidative half-reactions.

A numerical study of turbulent combustion systems was pursued to examine different computational modeling techniques, namely computational fluid dynamics (CFD) and chemical reactor network (CRN) methods. Both methods have been studied and analyzed as individual techniques as well as a coupled approach to pursue better understandings of the mechanisms and interactions between turbulent flow and mixing, ignition behavior and pollutant formation. A thorough analysis and comparison of both turbulence models and chemistry representation methods was executed and simulations were compared and validated with experimental works. An extensive study of turbulence modeling methods, and the optimization of modeling techniques including turbulence intensity and computational domain size have been conducted. The final CFD model has demonstrated good predictive performance for different turbulent bluff-body flames. The NOx formation and the effects of fuel mixtures indicated that the addition of hydrogen to the fuel and non-flammable diluents like CO2 and H2O contribute to the reduction of NOx. The second part of the study focused on developing chemical models and methods that include the detailed gaseous reaction mechanism of GRI-Mech 3.0 but cost less computational time. A new chemical reactor network has been created based on the CFD results of combustion characteristics and flow fields. The proposed CRN has been validated with the temperature and species emission for different bluff-body flames and has shown the capability of being applied to general bluff-body systems. Specifically, the rate of production of NOx and the sensitivity analysis based on the CRN results helped to summarize the reduced reaction mechanism, which not only provided a promising method to generate representative reactions from hundreds of species and reactions in gaseous mechanism but also presented valuable information of the combustion mechanisms and NOx formation. Finally, the proposed reduced reaction mechanism from the sensitivity analysis was applied to the CFD simulations, which created a fully coupled process between CFD and CRN, and the results from the reduced reaction mechanism have shown good predictions compared with the probability density function method. / Ph. D. / Turbulent combustion has been regarded as one of the most typical occurrences with industrial burners, where turbulent flow is produced by large vortex eddies when fuel and oxidizer mixes. Due to increasing demands for energy and concerns for environmental pollution, it is important to have a comprehensive understanding of turbulent combustion processes. To help provide information related to turbulent combustion, computational modeling can be used to give physical insights of the combustion process. A numerical study of turbulent combustion systems was pursued to examine different computational modeling techniques and to understand the mechanisms in terms of fluid dynamics and chemical kinetics. Computational fluid dynamics (CFD) was used to predict the flow field, including gas velocities, temperatures and fuel characteristics. Another computational technique known as the chemical reactor network (CRN) was used to provide information related to the chemical reactions and pollutant production. A method was developed as part of the study to couple the computational methods to pursue better understandings of the mechanisms and interactions between turbulent flow and mixing, ignition behavior and pollutant formation. Results have been compared with experimental data to optimize the modeling techniques and validate the developed model. The CRN model with the detailed gaseous reaction mechanism from the Gas Research Institute GRI-Mech 3.0 created a reacting network across the combustor with flame chemistry details. By post-processing the CRN results using a sensitivity analysis, the reduced reaction mechanism was summarized, which provided a promising method to generate representative reactions of the system from hundreds of species and reactions that occur in the combustion process. The proposed reduced reaction mechanism was applied to the CFD simulations, which created a fully coupled process between CFD and CRN. The results from the reduced reaction mechanism have shown good predictions compared with the probability density function method, which is a simplified way to model combustion. Pollutant emission such as NOx has also been studied in both CFD and CRN models, in terms of the effects of fuel mixtures, the formation mechanisms and influential factors as well as reactions to the formation process. The work provides guidance for an integrated framework to model and study turbulence and chemical reactions for turbulent combustion systems.

The study of the biosynthetic logic of natural products has established itself to be one of the more exciting areas of research and have become an important part of modern drug discovery and development efforts. Therefore, understanding the pathway and the chemical mechanism of the biosynthesis of natural products is important in that knowledge on these processes can be applied for combinatorial biosynthesis to generate new natural product derivatives with enhanced biological activities. In addition to the practical value, a lot of unprecedented chemical mechanisms can be found in the enzymes involved therein, which will significantly advance our understanding of enzyme catalysis. The works described in this dissertation focus on elucidating the chemical mechanism of a number of enzymes involved in natural product biosynthesis by utilizing the versatility of synthetic chemistry to prepare enzyme substrates and mechanistic probes. First, SpnF and SpnL responsible for constructing the tetracyclic architecture of spinosyn A have been investigated. In vitro assay revealed the importance of the highly conjugated system for the [4+2]cycloaddition catalyzed by SpnF. Biochemical studies strongly suggest that SpnL employs the Rauhut-Currier mechanism for the second cyclization step in the biosynthesis of spinosyn A. It was also demonstrated that SpnL requires SAM for its activity. Second, a radical SAM enzyme DesII involved in the desosamine pathway has been investigated. It has been demonstrated that DesII can catalyze the dehydrogenation of TDP-D-quinovose as well as the deamination of the natural substrate, which makes DesII unique among radical SAM enzymes. In vitro assays revealed that DesII requires stoichiometric amount of SAM, which. EPR study firmly established the intermediacy of a C-3 radical in the DesII-catalyzed dehydrogenation of TDP-D-quinovose. Finally, the chemical mechanism of AXS responsible for the biosynthesis of UDP-apiose has been investigated. In vitro activity assay using UDP-2F-glucuronic acid showed that the analog is a competitive inhibitor of AXS. A coupled assay strategy was also developed to investigate the chemical mechanism of AXS in the reverse direction. In addition, the stereospecificity of two separate hydride transfer steps of AXS reaction has been firmly established. / text

A síntese e caracterização de sistemas hetero-híbridos gerados a partir da 3,6-bi-2-piridil-1,2,4,5-tetrazina (bptz) e interações com ouro nanoparticulado são abordados nesta tese. O bptz foi estudado por meio de métodos espectroscópicos e teóricos, focalizando principalmente o efeito SERS associado à adsorção em nanopartículas de ouro. O mecanismo de transferência de carga para metais macroscópicos foi transposto para a condição nanoparticulada, envolvendo ligações químicas entre bptz e as nanopartículas. Os complexos estudados possuem fórmula geral [LmRu(µ-bptz)RuLm]Xn, com “L” indicando os ligantes periféricos 5-cloro-1,10-fenantrolina (Clphen) ou 4’-(fenil)-2,2&#8217:6&#8217,2&#8221-terpirdina (ptpy) e “X” os contra-íons. Foram investigadas suas espectroeletroquímicas eletrônica e SERS, e as mudanças de perfil vibracional foram modeladas, incorporando o mecanismo de transferências de carga entre complexo e o ouro, além dos mecanismos ressonantes e eletromagnéticos / The synthesis and investigation of heterohybrid systems encompassing 3,6-bi-2-pyridyl-1,2,4,5-tetrazine (bptz) and its ruthenium complexes associated with gold nanoparticles are dealt with in this thesis. Bptz was characterized by spectroscopic and theoretical techniques, focusing on its SERS spectra after the adsorption onto nanoparticles. The charge transfer mechanism in the SERS spectra of macroscopic metals was transposed to the nanoparticle condition, assuming the formation of chemical bonds between bptz and the nanoparticles. Complexes of general formula [LmRu(µ--bptz)RuLm]Xn, “L” the peripheric ligants 5-chlorine-1,10-phenantroline or 4’-(phenyl)-2,2&#8217:6&#8217,2&#8221-terpyrdine (ptpy), and “X” counter-ions were also investigated, with special emphasis on their electronic and SERS spectroelectrochemistry. The changes in the vibrational profiles were successfully explained by the occurrence of charge transfer between the adsorbed complex and gold, in addition to the electromagnetic and resonance mechanisms.

A síntese e caracterização de sistemas hetero-híbridos gerados a partir da 3,6-bi-2-piridil-1,2,4,5-tetrazina (bptz) e interações com ouro nanoparticulado são abordados nesta tese. O bptz foi estudado por meio de métodos espectroscópicos e teóricos, focalizando principalmente o efeito SERS associado à adsorção em nanopartículas de ouro. O mecanismo de transferência de carga para metais macroscópicos foi transposto para a condição nanoparticulada, envolvendo ligações químicas entre bptz e as nanopartículas. Os complexos estudados possuem fórmula geral [LmRu(µ-bptz)RuLm]Xn, com “L” indicando os ligantes periféricos 5-cloro-1,10-fenantrolina (Clphen) ou 4’-(fenil)-2,2&#8217:6&#8217,2&#8221-terpirdina (ptpy) e “X” os contra-íons. Foram investigadas suas espectroeletroquímicas eletrônica e SERS, e as mudanças de perfil vibracional foram modeladas, incorporando o mecanismo de transferências de carga entre complexo e o ouro, além dos mecanismos ressonantes e eletromagnéticos / The synthesis and investigation of heterohybrid systems encompassing 3,6-bi-2-pyridyl-1,2,4,5-tetrazine (bptz) and its ruthenium complexes associated with gold nanoparticles are dealt with in this thesis. Bptz was characterized by spectroscopic and theoretical techniques, focusing on its SERS spectra after the adsorption onto nanoparticles. The charge transfer mechanism in the SERS spectra of macroscopic metals was transposed to the nanoparticle condition, assuming the formation of chemical bonds between bptz and the nanoparticles. Complexes of general formula [LmRu(µ--bptz)RuLm]Xn, “L” the peripheric ligants 5-chlorine-1,10-phenantroline or 4’-(phenyl)-2,2&#8217:6&#8217,2&#8221-terpyrdine (ptpy), and “X” counter-ions were also investigated, with special emphasis on their electronic and SERS spectroelectrochemistry. The changes in the vibrational profiles were successfully explained by the occurrence of charge transfer between the adsorbed complex and gold, in addition to the electromagnetic and resonance mechanisms.