<p> This dissertation contains simulations of chemical catalysis in both biological and heterogeneous contexts. A mixture of classical, quantum, and hybrid techniques are applied to explore the energy profiles and compare possible chemical mechanisms both within the context of human and bacterial enzymes, as well as exploring surface reactions on a metal catalyst. A brief summary of each project follows. </p><p> Project 1 - Bacterial Enzyme SpvC </p><p> The newly discovered SpvC effector protein from <i>Salmonella typhimurium </i> interferes with the host immune response by dephosphorylating mitogen-activated protein kinases (MAPKs) with a &beta;-elimination mechanism. The dynamics of the enzyme substrate complex of the SpvC effector is investigated with a 3.2 ns molecular dynamics simulation, which reveals that the phosphorylated peptide substrate is tightly held in the active site by a hydrogen bond network and the lysine general base is positioned for the abstraction of the alpha hydrogen. The catalysis is further modeled with density functional theory (DFT) in a truncated active-site model at the B3LYP/6-31 G(d,p) level of theory. The truncated model suggested the reaction proceeds via a single transition state. After including the enzyme environment in <i>ab initio</i> QM/MM studies, it was found to proceed via an E1cB-like pathway, in which the carbanion intermediate is stabilized by an enzyme oxyanion hole provided by Lys104 and Tyr158 of SpvC. </p><p> Project 2 - Human Enzyme CDK2 </p><p> Phosphorylation reactions catalyzed by kinases and phosphatases play an indispensable role in cellular signaling, and their malfunctioning is implicated in many diseases. Ab initio quantum mechanical/molecular mechanical studies are reported for the phosphoryl transfer reaction catalyzed by a cyclin-dependent kinase, CDK2. Our results suggest that an active-site Asp residue, rather than ATP as previously proposed, serves as the general base to activate the Ser nucleophile. The corresponding transition state features a dissociative, metaphosphate-like structure, stabilized by the Mg(II) ion and several hydrogen bonds. The calculated free-energy barrier is consistent with experimental values. </p><p> Project 3 - Bacterial Enzyme Anthrax Lethal Factor </p><p> In this dissertation, we report a hybrid quantum mechanical and molecular mechanical study of the catalysis of anthrax lethal factor, an important first step in designing inhibitors to help treat this powerful bacterial toxin. The calculations suggest that the zinc peptidase uses the same general base-general acid mechanism as in thermolysin and carboxypeptidase A, in which a zinc-bound water is activated by Glu687 to nucleophilically attack the scissile carbonyl carbon in the substrate. The catalysis is aided by an oxyanion hole formed by the zinc ion and the side chain of Tyr728, which provide stabilization for the fractionally charged carbonyl oxygen. </p><p> Project 4 - Methanol Steam Reforming on PdZn alloy </p><p> Recent experiments suggested that PdZn alloy on ZnO support is a very active and selective catalyst for methanol steam reforming (MSR). Plane-wave density functional theory calculations were carried out on the initial steps of MSR on both PdZn and ZnO surfaces. Our calculations indicate that the dissociation of both methanol and water is highly activated on flat surfaces of PdZn such as (111) and (100), while the dissociation barriers can be lowered significantly by surface defects, represented here by the (221), (110), and (321) faces of PdZn. The corresponding processes on the polar Zn-terminated ZnO(0001) surfaces are found to have low or null barriers. Implications of these results for both MSR and low temperature mechanisms are discussed.</p>

<p> Transition-metal catalysis has enabled the development of an unprecedented number of mild and selective C-C bond-forming reactions. We sought to access the reactivity of palladium and nickel catalysts for two types of transformations: conjugate allylations and sp³-sp³ cross-coupling reactions. </p><p> Conjugate allylation of malononitriles was evaluated with N-heterocyclic carbene-ligated palladium complexes. The allylation was found to yield a variety of mono-allylated products. These results are in contrast to the bis-allylation of malononitriles using other palladium-based catalysts. Additionally, conjugate addition of &alpha;,&beta;-unsaturated <i>N</i>-acylpyrroles was found to be accelerated in the presence of sulfoxide substitution on the pyrrole ring. These substrates are lead compounds for the development of an enantioselective allylation reaction. </p><p> Transition metal-catalyzed cross-coupling reactions have become standard practice in organic synthesis. Recent advances in alkyl-alkyl couplings have been transformative in the way organic chemists approach the construction of target molecules. This dissertation focuses on the development of stereospecific sp³-sp³ cross-coupling reactions. We discovered that in the presence of nickel catalysts, secondary benzylic ethers were found to undergo stereospecific substitution reactions with Grignard reagents. Reactions proceeded with inversion of configuration and high stereochemical fidelity. This reaction allows for facile enantioselective synthesis of biologically active diarylethanes from readily available optically enriched carbinols. </p><p> Subsequently, this reaction was expanded to dialkylzinc reagents and the first stereospecific Negishi cross-coupling reaction of secondary benzylic esters was developed. A series of traceless directing groups were evaluated for their ability to promote cross-coupling with dimethylzinc. Esters with a chelating thioether derived from commercially-available 2-(methylthio)acetic acid were found to be the most effective. The products were formed in high yield and with excellent stereospecificity. A variety of functional groups were tolerated in the reaction including alkenes, alkynes, esters, amines, imides, and <i>O</i>-, <i>S</i>-, and <i>N</i>-heterocycles. The utility of this transformation was highlighted in the enantioselective synthesis of a retinoic acid receptor (RAR) agonist.</p>

<p> Several metal-tetracyanoethylene (TCNE) compounds, including the [bis(pentamethylcyclopentadienyl)iron(III)][tetracyanoethylene], [FeCp*²][TCNE], family of molecule-based magnets and two cyanide based MBMs were investigated by pressure dependent DC magnetic measurements. The 0-D electron transfer salts: [FeCp*²][TCNE], ferromagnetic [FeCp*²][TCNQ] (TCNQ = 7,7,8,8-tetracyanoquinodimethane), metamagnetic [FeCp*²][TCNQ], [FeCp*²][HCBD] (HCBD = hexacyanobutadiene), and [FeCp*²][DDQ] (DDQ = 2,3-dichloro-5,6-dicyano-p-benzoquinone) exhibited an array of magnetic behavior both at ambient and applied pressure. [FeCp*²][TCNE] and [FeCp*²][HCBD] exhibited weak ferromagnetism above 4.2 and 3.1 kbar, respectively. The ferromagnetic polymorph of [FeCp*²][TCNQ] displayed linear increase to the critical temperature, <i>T</i>_c, and the bifurcation temperature, <i>T</i>_b, reaching 5.01 and 5.46 K, respectively at 10.3 kbar. The coercive field, <i>H</i>_cr, displayed exponential-like increase, reaching 550 Oe at 10.3 kbar. The metamagnetic polymorph of [FeCp*²][TCNQ] displayed linear increase of the Tc at low applied pressure, reaching 2.90 at 2.9 kbar, then transitioned to a paramagnetic state at further applied pressure. [FeCp*²][HCBD] transitioned from a paramagnetic state at ambient pressure to a weak ferromagnetic state at 3.1 kbar with a <i>T</i>_c, <i>H</i>_cr, and <i>H</i>_c of 2.46 K, 25 Oe, and 2,200 Oe, respectively. The <i>T</i>_c and <i>H</i>_c then increased linearly with further applied pressure to 4.80 K and 10,000 Oe, while the <i>H</i>_cr increased exponentially to 795 Oe, at 11.4 kbar. [FeCp*²][DDQ] exhibited paramagnetic behavior at ambient and applied pressures up to 9.2 kbar. The structurally related 2-D Mn^II(TCNE)I(H₂O) and 3-D MnII(TCNE)_3/2(I₃)_1/2, showed significant increases to the <i> T</i>_c, T_b, and <i>H</i>_cr with applied pressure. A high- and low-pressure regions were observed for Mn^II(TCNE)I(H₂O). 2-D [Ru₂(O₂CBu^t)₄][M(CN)₆] &middot; H2O (M = Fe, Cr) displayed suppression of hysteretic properties at high applied pressure and irreversibility of the suppression. A Mean Field (MF) analysis of three structurally related non-cubic Prussian blue analogues (PBA) was performed to assess the intensity of their coupling modes. These values were framed by the reinvestigation of several known cubic PBAs and comparing the coupling intensities, as well as evaluating the MF theory in the context of these structures as several had been evaluated by other means.</p>

<p> A promising renewable energy scenario involves utilizing microalgae as biological solar cells to capture the energy in sunlight and then harvesting the biomass for renewable energy production. Through photosynthesis photons are captured by light-sensitive pigment molecules and used to create a cellular chemical energy gradient. Microalgae ultimately use this energy gradient to drive their metabolism by reducing inorganic carbon into renewable, energy-rich organic hydrocarbon stores such as triacylglycerols (TAGs). These valuable molecules act as a cellular energy reserve, readily drawn from when required, often forming large oil-bodies within microalgal cells that can be abundant in certain oleaginous species. This is important for biofuel production because lipids can be extracted from biomass and then converted into a variety of biofuels such as renewable diesel and jet fuel. Thus, from a biofuels perspective, maximizing lipid productivity in selected microalgal feedstock strains is considered essential to the development of an economically viable algal biofuels industry. To achieve this, many current research and development efforts are directed towards genetically engineering well-characterized microalgae to optimize TAG production; however, this approach is a time-consuming, costly prospect and the number of well-characterized strains is relatively few, especially when compared to the number of known extant species. Alternatively, microalgal feedstock optimization could be more readily accomplished by taking advantage of the prodigious natural diversity of microalgae in the environment and identifying native strains of microalgae that, through natural selection, already possess key metabolic traits necessary for commercial feedstock development. Formulated on this premise, a collaborative project between the National Renewable Energy Laboratory (NREL) and the Colorado School of Mines (CSM) recently established and cryopreserved a clonal microalgal culture collection containing 360 unique strains with preliminary data regarding lipid accumulation and the growth potential of select isolates. The goal of this work has been to 1) perform a far more detailed characterization of the algal culture collection by developing high throughput screening procedures and tools for identifying fast-growing, oleaginous strains; and 2) gather further insight into the microalgal diversity found in the southwestern United States. Herein is described in detail the rationale, methods, results and conclusions of these efforts.</p>

<p> These studies combine crossed laser-molecular beam scattering, velocity map imaging and computation to study the thermal decomposition mechanisms of geminal dinitro energetic materials. In our experimental studies, we photolytically generate two key intermediates in the decomposition of such energetic materials, 2-nitro-2-propyl radical and 2-nitropropene by photodissociating 2-bromo-2-nitropropane at 193 nm. These intermediates were produced at high internal energies and access a number of competing unimolecular dissociation channels. The scattering and imaging experiments provided evidence for four photodissociation pathways of 2-bromo-2-nitropropane along with a total of twelve subsequent dissociations of the resulting intermediate. In addition to the experimental studies, extensive calculations were conducted at the G4//B3LYP/6-311++g(3df,2p) level to compute the energetics of these dissociation events. Interestingly, a novel transition state (TS) for NO loss was discovered for the 2-nitro-2-propyl radical, which has a reaction barrier substantially lower than a traditional nitro-nitrite isomerization mechanism would suggest. This pathway is only available to nitroalkyl radicals and is extremely exothermic. To confirm the presence of this novel TS in a real-world system, the potential energy surface (PES) of a new energetic material, 1,1-diamino-2,2-dinitroethene (FOX-7), was calculated. This PES confirms the presence of the novel NO loss TS in FOX-7; this new TS allows for a low energy pathway to the production of NO in the unimolecular decomposition of FOX-7. In addition, these calculations demonstrate that initial loss of NO is competitive with simple C-N bond fission in unsaturated energetic materials. This low barrier and high exothermicity may be responsible for the extensive NO production and energy release observed in energetic materials with geminal dinitro groups.</p>

Thesis (Ph. D.)--University of Connecticut, 2006. / (UnM)AAI3221565. Adviser: Glenn King. Source: Dissertation Abstracts International, Volume: 67-06, Section: B, page: 3122.

Practical knowledge, as defined by Freema Elbaz (1983), is a complex, practically oriented set of understandings which teachers use to actively shape and direct their work. The goal of this study is the construction of a social science portrait that illuminates the practical knowledge of a large lecture professor of general chemistry at a public research university in the southeast. This study continues Elbaz's (1981) work on practical knowledge with the incorporation of a qualitative and intentionally interventionist methodology which "blurs the boundaries of aesthetics and empiricism in an effort to capture the complexity, dynamics, and subtlety of human experience and organizational life," (Lawrence-Lightfoot and Davis, 1997). This collection of interviews, observations, writings, and reflections is designed for an eclectic audience with the intent of initiating conversation on the topic of the large lecture and is a purposeful attempt to link research and practice. Social science portraiture is uniquely suited to this intersection of researcher and researched, the perfect combination of methodology and analysis for a project that is both product and praxis. The following research questions guide the study. Are aspects of Elbaz's practical knowledge identifiable in the research conversations conducted with a large lecture college professor? Is practical knowledge identifiable during observations of Patricia's large lecture chemistry classroom practice? Freema Elbaz conducted research conversations with Sarah, a high school classroom and writing resource teacher who conducted much of her teaching work one on one with students. Patricia's practice differs significantly from Sarah's with respect to subject matter and to scale. / Ph. D.

Dealing with the college laboratory program in general chemistry, this study compares the effects of exercises based on current national problems with the effects of traditional laboratory exercises. The study has been prompted by the recent emphasis on topics of national interest in the undergraduate chemistry curriculum. These topics include air and water pollution, drug addiction and analysis, tetraethyl-lead additives, insecticides in the environment, and recycling of wastes. The relevant experiments are taken from recent issues of the Journal of Chemical Education. The traditional exercises, from the laboratory manual Chemistry in the Laboratory, by Watt, Hatch, and Lagowski (New York, Norton, 1964), deal with such topics as chemical composition, gas laws, solutions, and acids and bases.

Thesis (Ph. D.)--University of Illinois at Urbana-Champaign, 2006. / Source: Dissertation Abstracts International, Volume: 67-07, Section: B, page: 3643. Adviser: Neil L. Kelleher. Includes bibliographical references. Available on microfilm from Pro Quest Information and Learning.

This study investigated approaches to studying, intellectual developments, and metacognitive skills of general chemistry students enrolled for the spring 2011 semester at a single campus of a multi-campus community college. the three instruments used were the Approaches and Study Skills Inventory for Students (ASSIST), the Learning Environment Preferences (LEP), and the Executive Process Questionnaire (EPQ). the subjects were 138 students enrolled in either general chemistry 1 or 2. the results revealed that the preferred approach to study was the strategic approach. the intellectual development of the students was predominantly Perry’s position 2 (dualist) in transition to position 3 (multiplicity). Correlation statistics revealed that deep approach to studying is related to effective employment of metacognitive skills. Students with a deep approach to studying were likely to utilize effective metacognitive skills. Students with a surface approach to studying used no metacognitive skills or ineffective metacognitive skills. Multiple logistic regression analysis was conducted to ascertain which of the three variables, namely approaches to studying, ability to metacognate, or level of intellectual development, was the most salient in predicting the success of general chemistry students. No single variable was found to predict students’ success in general chemistry classes; however, a surface approach to studying predisposes general chemistry students to fail. the implication of this study is that students’ study approaches, intellectual developments, and metacognitive skills are requisite information to enable instructional remediation early in the semester.