We investigated the reactivity of difluorovinylidene groups (C2F2) on Cu(111) under ultrahigh vacuum conditions. Difluorovinylidene moieties bonded to surface were generated by the dissociative adsorption of 1,1-dibromodifluoroethylene. Temperature Programmed desorption (TPD) and reflection-adsorption infrared spectroscopy (RAIRS) revealed the thermal reaction pathways, and a variety of intermediates were identified or inferred. The major desorption product, hexafluoro-2-butyne (C4F6), was detected at 445 K. It invokes a step of fluoride addition to difluorovinylidene to render the intermediacy of C2F3. However, differences exist when the vibration data from F + C=CF2 were compared with those from C−CF3 and CF=CF2 in previous literature, implying that the form is neither ethylidyne nor vinyl. Based on the concept of fluorine hyperconjugation, density function theory (DFT) calculations were utilized to obtain two transition states, quasi-vinyl and -ethylidyne, which can account for the differences present in the IR spectra. The relative thermal stability follows the trend of vinyl > quasi-ethylidyne > quasi-vinyl > vinylidene > ethylidyne suggested by IR and DFT calculations. Finally, the end product, CF3C¡ÝCCF3, might be formed by coupling of two quasi-ethylidyne species via the partial allenic forms.

Computational methods have become an integral part of drug development and can help bring new and better drugs to the market faster. The process of predicting the biological activity of large compound collections is known as virtual screening, and has been instrumental in the development of several drugs today in the market. Computational methods can also be used to elucidate the energies associated with chemical reactivity and predict how to improve a synthetic protocol. These two applications of computational medicinal chemistry is the focus of this thesis. In the first part of this work, quantum mechanics has been used to probe the energy surface of palladium(II)-catalyzed decarboxylative reactions in order to gain a better understating of these systems (paper I-III). These studies have mapped the reaction pathways and been able to make accurate predictions that were verified experimentally. The other focus of this work has been to develop virtual screening methodology. Our first study in the area (paper IV) investigated if the results from several virtual screening methods could be combined using data fusion techniques in order to get a more consistent result and better performance. The study showed that the results obtained from data fusion were more consistent than the results from any single method. The data fusion methods also for several target had a better performance than any of the included single methods. Next, we developed a dataset suitable for evaluating the performance of virtual screening methods when applied to large compound collection as a replacement or complement for high throughput screening (paper V). This is the first benchmark dataset of its kind. Finally, a method for using computationally derived reaction coordinates as basis for virtual screening was developed. The aim was to find inhibitors that resemble key steps in the mechanism (paper VI). This initial proof of concept study managed to locate several known and one previously not reported reaction mimetics against insulin regulated amino peptidase.

As computational methods for the prediction of metallic nanoparticle structure and reactivity continue to advance, a need has developed for simple experimental models that can mimic and confirm theoretical predictions. Dendrimer-encapsulated nanoparticles, or DENs, are ideal to fill this role. DENs are synthesized within poly(amido amine) dendrimer templates which allows for the controlled synthesis of monodisperse nanoparticles in the 50-250 atom (1-2 nm) size range. These are small enough to be accessible to high-level theoretical calculations while being large enough to study experimentally. The research reported here consists of several independent but closely related studies. First, the synthesis, structural, and electrochemical properties of Au@Pt (core@shell) DENs are described. These materials are prepared by underpotentially depositing Cu onto Au DENs followed by galvanic exchange of Cu for Pt. Second, Pb UPD onto Au DENs and a detailed experimental and theoretical study of the resulting core@shell particle structures and catalytic activity is discussed. It is found that no matter how much Pt is deposited onto the surface of Au₁₄₇ DENs, a surface reorganization occurs resulting in similar electrocatalytic activity for the oxygen reduction reaction. Third, an in-depth X-ray absorption spectroscopy study of the structural properties of thiol-capped Au₁₄₇ DENs is described. Here, the surfaces of uncapped Au₁₄₇ nanoparticles are titrated with strongly binding thiol ligands to tune the extent of surface disorder. The effect of the increased surface disorder on the standard EXAFS fitting results is discussed from experimental and theoretical perspectives. Lastly, an in-situ electrochemical study of Au₁₄₇ DENs structure is reported. The key result is that the Au lattice expands during electrochemical surface oxidation. This is an important result for understanding electrocatalytic processes on Au nanoparticle / text

Oxide interfaces have attracted considerable attention in recent years due to emerging novel properties that do not exist in the corresponding parent compounds. Furthermore, modern atomic-scale growth and probe techniques enable the formation and study of new artificial interface states distinct from the bulk state. A central issue in controlling the novel behavior in oxide heterostructures is to understand how various physical variables (spin, charge, lattice and/or orbital hybridization) interact with each other. In particular, density function theory (DFT) has provided significant insight into underlying physics of materials at the atomic level, giving quantitative results consistent with experiment. In this dissertation using density functional theory methods, we explore the electronic, magnetic and structural properties developed near the interface in SrTiO3/LaAlO3, EuO/LaAlO3, Fe/PbTiO3/Pt, Fe//BaTiO3/Pt and Cs/SrTiO3 heterostructures. We study the interplay between physical interactions, and quantify parameters that determine physical properties of hetetrostructures. These theoretical studies help understanding how physical variables couple with each other and how they determine new properties at oxide interfaces. / text

A series of alkyldithiolatodiironhexacarbonyl complexes of the form &mu:-(RS2)Fe2(CO)6, where RS2 is: 1,2-ethanedithiolate (eth-cat), cis-1,2-cyclopentanedithiolate (pent-cat), cis-1,2-cyclohexanedithiolate (hex-cat), and 2-exo,3-exo-bicyclo[2.2.1]heptanedithiolate (norbor-cat), are reported. These complexes display structures and catalytic behavior toward production of molecular hydrogen with similarities to the active site of the diiron hydrogenase enzymes. Hydrogen production is desirable as an alternative fuel source and these catalysts are capable of producing H2 in the presence of weak acid under electrochemical conditions. Through understanding of the factors which control the catalytic activity of these catalysts it may be possible to contribute to the development of a hydrogen fuel economy.Significant scan-rate dependence under electrochemical conditions is observed, resulting in an initial 1-to-2 electron reduction depending on how quickly the singly reduced species can reorganize. The rate of this reorganization directly corresponds to the internal strain within the system and can be ranked in the following order of increasing rate of reorganization: pent-cat < norbor-cat < eth-cat < hex-cat. Additionally, these catalysts all successfully catalyze protons to molecular hydrogen under electrochemical conditions in the presence of acetic acid via an ECEC catalytic mechanism, where, E is an electrochemical step (reduction) and C is a chemical step (protonation).Density functional theory computations support the reported catalytic processes by calculating physically observable quantities, such as: pKa values, reduction potentials, adiabatic ionization energies and carbonyl stretching frequencies in the infrared (IR) region. These quantities were used to suggest reasonable reactive intermediates within the catalytic cycle. The electronic structure of each catalyst was examined using photoelectron spectroscopy and the global minimum cationic structure, in all cases, involves a structure with a bridging carbonyl ligand, akin to that of the enzyme active site.The most significant outcome of this work is the unprecedented diiron center rotation upon reduction. As conformational strain involving the dithiolate ligand increases, the rate of reorganization of the anion increases leading to cleavage of an iron-sulfur bond to provide an alternative protonation site, a key step toward molecular hydrogen formation. This site is less basic than the unrotated form and helps evolve H2 with thermodynamic favorability.

Memory arrays cannot be as easily tested as other storage elements in a chip. Most of the flip-flops (FFs) in a chip can be replaced by scan cells in scan-based design. However, the bits in memory arrays cannot be replaced by scan cells, due to the area cost and the timing-critical nature of many of the paths into and out of memories. Thus, bits in a memory array can be considered non-scan storage elements. Test methods such as memory built-in self-test (MBIST), functional test, and macro test are used to test memory arrays. However, these tests aren’t sufficient to test the paths through the memory arrays. During structural (scan) test generation, memory arrays are treated as “black boxes” or memory arrays are bypassed to a known value. Black boxes decrease coverage loss while bypassing increases chip area and delay. Path delay test through memory arrays is proposed using pseudo functional test (PFT) with K Longest Paths Per Gate (KLPG). In this technique, any longest path that is captured into a non-scan cell (including a memory cell) is propagated to a scan cell. The propagation of the captured value from non-scan cell to scan cell occurs during low-speed clock cycles. In this work, we assume that only one extra coda cycle is sufficient to propagate the captured value to a scan cell. This is true if the output of the memory feeds combinational logic that in turn feeds scan cells. When we want to launch a transition from a memory output, different values are written into different address locations and the address is toggled between the locations. The ATPG writes the different values into the memory cells during the preamble cycles. In the case of launching a transition out of a non-scan cell, the cell must be written with an initial value during the preamble cycles, and the next value set on the non-scan cell input. Thus, it is possible to capture and launch transitions into and from memory and non-scan cells and thus test the path delay of the longest paths into and out of memory and non-scan cells.

Ce travail a essentiellement porté sur la description et la rationalisation de certaines propriétés des complexes du Zinc contenant des ligands de base de Schiff par le biais d’approches mixtes théorique et expérimentale. La première partie de ce travail concerne la synthèse et la caractérisation d’un nouveau complexe dinucléaire de Zn(II) à ligand base de Schiff tétra-azoté N4. Ce complexe s’auto-assemble en hélice à double brin avec un environnement tétraédrique rarement observé pour l’ion Zn2+ avec ce type de ligand. Ce complexe s’est avéré être thermodynamiquement instable en présence de traces d’eau, subissant ainsi une démétallation rapide. De ce fait, sa réactivité vis-à-vis de l’eau a été étudiée par des mesures spectroscopiques et des calculs DFT. Puis, le mécanisme réactionnel de démétallation a été élucidé pour la première fois et pourrait facilement être généralisé à l’hydrolyse des complexes Zn-sal(ph)en apparentés. Dans la seconde partie, le caractère acide de Lewis, principal facteur de la réactivité/coordination des complexes Zn-sal(ph)en a été étudié au moyen des descripteurs de la DFT-conceptuelle. Une analyse préliminaire a été réalisée sur un prototype modèle à savoir [ZnCl4]2-, et les résultats ont été généralisés aux complexes de Zn-sal(ph)en comportant différents types d’espaceurs diamine (flexible, semi-rigide, et rigide) afin de rationaliser l’acidité de Lewis de ces complexes avec la nature du pont diamine. L’inclusion des densités des états excités par le biais du descripteur dual dit « state specific dual descriptor» a permis de décrire avec succès la réactivité appropriée du complexe choisi. Enfin, la troisième partie de ce travail, est consacré à l’effet dit de « self-interaction » survenue dans la modélisation de la réaction de cyclo-addition du CO2 sur les époxydes catalysée par un complexe Zn-N4 base de Schiff en présence de NBu4X (X=I). Cette erreur menant à des profils énergétiques irréalistes au niveau DFT, a été identifiée et une nouvelle approche théorique a été proposée et développée afin de contourner cette erreur / In this work, we focus our interest on the description and rationalization of some properties of Zinc complexes of Schiff bases schemes through theoretical and experimental approaches. The first study deals with the syntheses and characterization of a novel Zn-N4-Schiff base L= ((±) -trans-N, N’-Bis(2-aminobenzylidene)-1,2-diaminocyclohexane) showing an unexpected self-assembled double-stranded helicate structure , in which zinc atoms are in distorted tetrahedral environments, revealing an M- (R, R) left-handed helicity in its asymmetric unit. This dimer is thermodynamically unstable in presence of water traces and undergoes a rapid demetallation process that is studied by both experimental and theoretical approaches. The reaction is monitored through DOSY NMR analysis, and the theoretical mechanism of the demetallation process is elucidated for the first time using DFT method and which should be easily generalized to the demetallation of N2O2 sal(ph)en Zn complexes. In the second part of this study, the Lewis acidic behavior, the main factor of the reactivity/coordination of Zn-sal(ph)en complexes, is studied using conceptual density functional theory descriptors. This Lewis acidic character is addressed in a first stage to a prototype complex, namely [ZnCl4]2- and the results have been generalized to Zn-sal(ph)en complexes with different diamine bridges through flexible to semi-rigid then to rigid ranges, in order to characterize and rationalize this Lewis acid effect in relation with the nature of the diamine bridge. The inclusion of the electronic excited state densities by the so-called state specific dual descriptor allows us to recover successfully the appropriate reactivity of these chosen complexes. Finally, in the third part, we consider the effect of the « self-interaction » occurring when modeling the cycloaddition of CO2 to epoxide reactions catalyzed via the binary system Zn-N4 Schiff base /NBu4X (X=I). This error leading to unrealistic energy profiles at the DFT level has been identified and a new theoretical approach is proposed and developed to correct this error

Chiral phosphoric acids are bifunctional catalysts that have the ability to activate electrophiles and nucleophiles through hydrogen bonding, and they have been successful in catalysing highly enantioselective additions of a wide range of nucleophiles to imines. In most literature reports it is not frequently revealed how these catalysts impart enantioselectivity. Thus, the vast majority of time required for reaction development is expended on the optimisation of the catalyst features. The research described here explores the ability of relating computational derived catalyst parameters to enantioselectivity as a means to assess the catalyst features important for enantioinduction. The proposed features are evaluated computationally and summarised into simple qualitative models to understand and predict outcomes of similar reactions. In Chapter 1, I provide an overview of the progress and challenges in the development of chiral phosphoric acid mediated reactions. I highlight leading computational studies that have enabled a greater understanding of how the catalyst imparts reactivity and selectivity. In general, the studies focus on the most effective catalyst and do not do a detailed investigation into the effects of changing the substituents at the 3,3’ positions. Implicating steric effects from reasonably large groups as a key component in imparting enantioselectivity. However, it is clear that they have a more subtle effect. A large group is required but if it is too large poor or unusual results are obtained, making the correct choice of reaction conditions challenging. In Chapter 2, I develop a quantitative assessment of the substituents at the 3,3’ positions. I show in Chapters 3 and 4 that I can use rotation barriers in combination with a novel steric parameter, AREA(θ), to correlate enantioselectivity. By exploiting this finding, the catalyst features important for enantioselectivity can be identified, and this is validated by QM/MM hybrid calculations. Summarising these detailed calculations into a single qualitative model, guides optimal catalyst choice for all seventy-seven literature reactions reporting over 1000 transformations. These mechanistic studies have guided the design of a new catalyst with increased versatility, which is discussed in Chapter 5. Chapter 6 details my study into the effect of the hydroxyl group on the mechanism of transfer hydrogenation of imines derived from ortho-hydroxyacetophenone. I show, using detailed DFT and ONIOM calculations, that transition states of these reactions involve hydrogen bonding from both the hydroxyl group on the imine and the nucleophile’s proton to the phosphate catalyst. In Chapter 7, computational analysis is used to provide insight into the origins of enantioselectivity in chiral phosphoric acid catalysed Friedel-Crafts and Mannich reactions proceeding through monoactivation mechanisms. The final chapter contains an in-depth look into the stereoelectronic effects altering enantioselectivity in the silver-phosphate mediated spirocyclisation reaction involving aromatic ynones. In this study I show that enantioselectivity is governed by the non-covalent interactions between the aromatic group of the ynone and the 3,3’ substituent. I was able to propose synthetic modifications to the substrate used in this reaction, resulting in an improvement in enantioselectivity.

The basis of prosperity of 20th centrury is oil. As oil is going to be used up, people need to find alternatives to meet the earth’s energy demand in 21st centrury. For each second, there are about 1.2×1017 J energy hitting the earth. The energy in 1 hour of sunlight is about 4.32×1020 J, which almost meets the energy consumed on earth in 2016. It determines solar energy may be a potential candidate to solve the energy crisis. As for techniques to utilize solar energy, the most popular one is using photovoltaic (PV) cells. PV cell is a device to convert solar energy into electricity. There are also some other techniques trying to utilize solar energy. Photocatalysis is one of them, which is to convert solar energy into chemical energy. Applications of photocatalysis have extended from hydrogen evolution via water splitting to environemtnal remediation, CO2/ N2 reduction and so on. Photocatalysis, as an advanced oxidation process, has been extensively studied and applied to the purification and remediation of contaminated water and wastewater, and exhibits advantages over conventional treatment technologies. When considering solar energy as an energy source for photocatalysis, it is key to prepare visible light-responsive materials. Bismuth-based semiconductors are promising materials as visible light-responsive photocatalysts primarily due to their suitable band gaps, well-dispersed valence bands, and commercial availabilities at reasonable costs, as well as the possibility of preparing them under mild conditions. Recent work focusing on the preparation, characterization and activity testing of bismuth-based photo-active materials as well as their associated photoreactor designs are introduced herein. In order to enhance the photocatalytic activities of the new materials, different precursors, additives, preparation procedures and process parameters, as well as surface treatments were explored to obtain binary and ternary heterostructures, with different doping, surface modification, nanoparticle sizes and morphologies. It was found that formation of heterojunction and loading metal nanoparticle on the surface are very effective to imrove the photocatalytic activity of the support. In this work, we found that palladium nanoparticles modified BiVO4 exhibited excellent activity in the decomposition of phenol, which was even higher than TiO2. To facilitate the separation process of catalysis particels from a slurry system, magnetically separable composites were also prepared, and it was found that it is very effective to remove the particles from the slurry system using external magnets. To further scale up this process, two different types of immbolized photoreactors (flat-plate and packed beads photoreactor) were also developed. Suggestions were made for further work in this research area.

SERAFIM, Leonardo Farias. Estudo experimental e computacional das propriedades vibracionais e citotóxicas de nutracêuticos do alho. 2015. 120 f. Dissertação (Mestrado em química)- Universidade Federal do Ceará, Fortaleza-CE, 2015. / Submitted by Elineudson Ribeiro (elineudsonr@gmail.com) on 2016-10-11T15:39:01Z No. of bitstreams: 1 2015_dis_lfserafim.pdf: 6533069 bytes, checksum: bd4393ac51b8c03b2234e51cb174e97a (MD5) / Approved for entry into archive by Jairo Viana (jairo@ufc.br) on 2016-10-11T23:50:48Z (GMT) No. of bitstreams: 1 2015_dis_lfserafim.pdf: 6533069 bytes, checksum: bd4393ac51b8c03b2234e51cb174e97a (MD5) / Made available in DSpace on 2016-10-11T23:50:48Z (GMT). No. of bitstreams: 1 2015_dis_lfserafim.pdf: 6533069 bytes, checksum: bd4393ac51b8c03b2234e51cb174e97a (MD5) Previous issue date: 2015 / The cytotoxic and bactericidal activities of garlic extract were tested in three tumor cell lines (HCT-166, SF-295 e OVCAR-8) and four bacteria cultures: two gram-positives (Staphylococcus aureus ATCC 25923 and Staphylococcus epidermidis ATCC 12228) and two gram-negatives (Pseudomonas aeruginosa ATCC 9027 e Escherichia coli ATCC 11303). Aiming to improve the bioavailability and cell targeting (tumor or bacteria) of these nutraceuticals, a drug delivery system based on the adsorption of garlic extract on calcium carbonate microparticles was developed. Additionally, computer simulations within the Density Functional Theory (DFT) formalism were accomplished to find the structural and vibrational properties of two molecules, alliin and methiin, present in garlic extract. alliin the highest concentration specie present in garlic extract was used as theoretical model to represent the garlic extract on the potential interaction calculations with calcium carbonate microparticles. The computer codes GAUSSIAN, Forcite and Dmol3, with the Meta hybrid M06-2X and the pure GGA-PBE Exchange-correlation functional were used to implement the computations. The vibrational spectra recorded for the alliin unveiled intense absorption peaks at: 1637, 1592, 1519, 1430, 1397, 1390, 1357 1018, 544 cm-1 on IR spectrum, mainly assigned to the carboxyl, amine and sulfoxide groups vibrations, and at 1643, 1429, 1404, 1316, 1297, 1207, 790, 744, 693, 588, 503 cm-1 on Raman spectrum, associated to the carbon chain vibrations. The methiin IR spectrum is similar to alliin’s, but, its Raman spectrum unveiled absorption bands which may differentiate both molecules, mainly for the absence of the absorption peak observed at 1643 cm-1 , ascribed to the allyl group vibration. The calculated theoretical vibrational spectra showed a good agreement with the experimental data. The interaction potential calculations suggests the adsorption of at least four solvation layers of the nutraceuticals around the calcium carbonate microparticles, this fact allow the slowly release of the species, preserving its bioavailability. The cytotoxicity tests showed tumor cells growth inhibition of 93% for the three tumor cell line studied, and bactericidal activity on gram-positives bacteria cell cultures, which proved the synergetic effect of garlic extract with calcium carbonate and its efficacy as drug delivery system. Those results shows the application potential of the calcium carbonate microparticles modified with garlic extract on the treatment of cancer and as antibacterial agent. / A atividade citotóxica e bactericida do extrato de alho, em três linhagens de células tumorais (HCT-166, SF-295 e OVCAR-8) e em quatro culturas de bactérias: duas gram-positivas (Staphylococcus aureus ATCC 25923 e Staphylococcus epidermidis ATCC 12228) e duas gram-negativas (Pseudomonas aeruginosa ATCC 9027 e Escherichia coli ATCC 11303), foi investigada neste trabalho. Visando melhorar a biodisponibilidade e o direcionamento destes nutracêuticos para células alvo (tumores ou bactérias), um sistema de liberação de fármacos baseado na adsorção do extrato de alho em micropartículas de carbonato de cálcio foi desenvolvido. Adicionalmente, simulações computacionais no formalismo DFT (Density Functional Theory) foram realizadas para a determinação das propriedades estruturais e vibracionais de duas moléculas, alliina e metiina, presentes neste extrato aquoso. A molécula de alliina, espécie de maior concentração no extrato aquoso utilizado, foi usada como modelo teórico para cálculos de potenciais de interação do extrato de alho e das micropartículas de carbonato de cálcio. Os códigos GAUSSIAN, Forcite e Dmol3, assim como o funcional meta-híbrido M06-2X e o funcional puro GGA na sua formulação BPE foram usados nas simulações. Os espectros vibracionais obtidos para a molécula de alliina revelaram intensas absorções em: 1637, 1592, 1519, 1430, 1397, 1390, 1357 1018, 544 cm-1 na região do infravermelho, principalmente associadas a vibrações dos grupos carboxila, amino e sulfóxido, e em: 1643, 1429, 1404, 1316, 1297, 1207, 790, 744, 693, 588, 503 cm-1 no espectro Raman, associados a vibrações da cadeia carbônica. O espectro na região do infravermelho da molécula de metiina é semelhante ao da alliina, porém, seu espectro Raman revela bandas de absorção que podem diferenciar as duas espécies, principalmente a ausência do pico observado em 1643 cm-1 reverente ao grupo alila. Os espectros vibracionais teóricos calculados indicam uma ótima correlação com os espectros experimentais obtidos, tanto paras moléculas puras como para o extrato produzido em laboratório. Os cálculos de potenciais de interação sugerem a adsorção dos nutracêuticos em pelo menos quatro camadas de solvatação em torno das micropartículas de carbonato de cálcio, o que promove sua lenta liberação, elevando sua biodisponibilidade. Os testes de citotoxicidade revelaram inibição do crescimento tumoral de cerca de 93%, nas as três linhagens de células tumorais, e atividade bactericida nas duas colônias de bactérias gram-positivas estudadas, o que comprovou o efeito sinergético do extrato de alho com o carbonato de cálcio e sua eficácia como sistema de liberação de nutracêuticos. Estes resultados demonstram o potencial de aplicação na prática farmacêutica do uso de micropartículas de carbonato de cálcio modificadas com extrato de alho para combate a células tumorais e a ações bactericidas